NM_001136020.3:c.1060+3883T>G

Variant names:

• chr7-8134957-A-C
• rs4725072
• NM_001136020.3:c.1060+3883T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136020.3(ICA1):​c.1060+3883T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.959 in 152,222 control chromosomes in the GnomAD database, including 70,026 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 0.96 (70026 hom., cov: 30)
• Consequence: ICA1 NM_001136020.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136020.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ICA1	NM_001136020.3	MANE Select	c.1060+3883T>G		intron	N/A	NP_001129492.1	A0A024RA29
	ICA1	NM_001350826.2		c.1147+3883T>G		intron	N/A	NP_001337755.1	Q05084-2
	ICA1	NM_001350827.2		c.1147+3883T>G		intron	N/A	NP_001337756.1	Q05084-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ICA1	ENST00000402384.8	TSL:2 MANE Select	c.1060+3883T>G		intron	N/A	ENSP00000385570.3	Q05084-1
	ICA1	ENST00000422063.6	TSL:1	c.1147+3883T>G		intron	N/A	ENSP00000403982.2	Q05084-2
	ICA1	ENST00000396675.7	TSL:1	c.1060+3883T>G		intron	N/A	ENSP00000379908.3	Q05084-1

Frequencies

GnomAD3 genomes AF: 0.959 AC: 145864 AN: 152104 Hom.: 69967 Cov.: 30

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.957

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

GnomAD4 genome AF: 0.959 AC: 145982 AN: 152222 Hom.: 70026 Cov.: 30 AF XY: 0.961 AC XY: 71504 AN XY: 74418

African (AFR) AF: 0.987 AC: 41016 AN: 41540

American (AMR) AF: 0.962 AC: 14715 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3383 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5180 AN: 5186

South Asian (SAS) AF: 0.958 AC: 4622 AN: 4824

European-Finnish (FIN) AF: 0.966 AC: 10213 AN: 10568

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63726 AN: 68014

Other (OTH) AF: 0.957 AC: 2023 AN: 2114

Alfa AF: 0.946 Hom.: 30399

Bravo AF: 0.961

Asia WGS AF: 0.986 AC: 3429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.79
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4725072; hg19: chr7-8174587;