Toward a clinical diagnostic pipeline for SPINK1 intronic variants

Tang, Xin-Ying; Lin, Jin-Huan; Zou, Wen-Bin; Masson, Emmanuelle; Boulling, Arnaud; Deng, Shun-Jiang; Cooper, David N.; Liao, Zhuan; Férec, Claude; Li, Zhao-Shen; Chen, Jian-Min

doi:10.1186/s40246-019-0193-7

Human Genomics

Table 1 SPINK1 deep intronic variants found in the 52 Chinese patients with chronic pancreatitis

From: Toward a clinical diagnostic pipeline for SPINK1 intronic variants

Intron	Variant		No. of carriers^a	Allele frequency in patients	Allele frequency in the East Asian population^b	rs number	In silico prediction^c	In vitro validation
Intron	cDNA numbering	gDNA numbering (chr 5, hg19)	No. of carriers^a	Allele frequency in patients	Allele frequency in the East Asian population^b	rs number	In silico prediction^c	In vitro validation
Minor allele frequency of ≥ 5% (all have previously been described [3])
2	c.88-352A > G	g.147208043 T > C	51 (37 hom.)	0.846	0.819^d	rs6580502	No effect	Not done
3	c.194 + 1159C > G	g.147206426G > C	10	0.096	0.070	rs1897577	No effect	Not done
3	c.195-1645G > C	g.147205914C > G	43 (17 hom.)	0.577	0.571^d	rs17717320	No effect	Not done
3	c.195-1570C > A	g.147205839G > T	44 (22 hom.)	0.635	0.619^d	rs17703305	No effect	Not done
3	c.195-478 T > G	g.147204747A > C	10	0.096	0.070	rs17774073	No effect	Not done
3	c.195-323C > T	g.147204592G > A	44 (21 hom.)	0.625	0.618^d	rs4705202	No effect	Not done
Minor allele frequency of < 5% (all have not previously been described [3])
1	c.56-609G > C	g.147209802C > G	1	0.00962	Absent from genomAD	Not available	No effect	Not done
1	c.56-324 T > A	g.147209517A > T	2	0.01923	0.00963	rs546549375	No effect	Yes
3	c.194 + 671C > T	g.147206914G > A	1	0.00962	0.00193	rs889082209	No effect	Not done
3	c.194 + 723C > T	g.147206862G > A	1	0.00962	0.00193	rs573757839	No effect	Not done
3	c.194 + 855G > A	g.147206730C > T	1	0.00962	0.00705	rs543534355	No effect	Not done
3	c.194 + 1278C > T	g.147206307G > A	3	0.02885	0.01797	rs118005432	No effect	Yes
3	c.194 + 1599G > A	g.147205986C > T	1	0.00962	Absent from genomAD	Not available	No effect	Not done
3	c.195-1414 T>A^e	g.147205683A>T^e	1	0.00962	0.00000^f	rs2436411^e	No effect	Yes
3	c.195-862 T > C	g.147205131A > G	1^g	0.01923	Absent from genomAD	Not available	No effect	Yes
3	c.195-854C > T	g.147205123G > A	1	0.00962	0.00062	rs1055746254	No effect	Yes

^aNumber of homozygotes (hom.) is indicated in parentheses wherever applicable
^bData are in accordance with genomAD (as of October 31, 2018)
^cEffect on spice site selection predicted by SpliceSiteFinder-like, MaxEntScan, NNSPLICE and GeneSplicer under default conditions
^dThe alternative minor allele frequency is of ≥ 5%
^eIn hg19, the reference sequence at this position is the minor allele sequence
^fAbsent in the East Asian population but present in other population(s)
^gThe carrier is a homozygote. The presence of a large deletion spanning the position of interest cannot be excluded

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