rs3823831

Positions:

• chr7-8200807-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136020.3(ICA1):​c.579+17498G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,158 control chromosomes in the GnomAD database, including 12,214 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (12214 hom., cov: 33)
• Consequence: ICA1 NM_001136020.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

Genes affected

ICA1 (HGNC:5343): (islet cell autoantigen 1) This gene encodes a protein with an arfaptin homology domain that is found both in the cytosol and as membrane-bound form on the Golgi complex and immature secretory granules. This protein is believed to be an autoantigen in insulin-dependent diabetes mellitus and primary Sjogren's syndrome. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Feb 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ICA1	NM_001136020.3	c.579+17498G>A		intron_variant		ENST00000402384.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ICA1	ENST00000402384.8	c.579+17498G>A		intron_variant		2	NM_001136020.3	A1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44520 AN: 152040 Hom.: 12176 Cov.: 33

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.253

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.293 AC: 44618 AN: 152158 Hom.: 12214 Cov.: 33 AF XY: 0.283 AC XY: 21081 AN XY: 74396

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0376

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.251

Alfa AF: 0.182 Hom.: 1400

Bravo AF: 0.325

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3823831; hg19: chr7-8240437;