rs10188961

Variant names:

• chr2-4879003-G-A
• rs10188961

Variant summary

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

The variant allele was found at a frequency of 0.584 in 152,020 control chromosomes in the GnomAD database, including 26,163 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 0.58 (26163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88626 AN: 151900 Hom.: 26126 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.584 AC: 88716 AN: 152020 Hom.: 26163 Cov.: 32 AF XY: 0.590 AC XY: 43793 AN XY: 74286

African (AFR) AF: 0.524 AC: 21745 AN: 41468

American (AMR) AF: 0.671 AC: 10250 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2384 AN: 3472

East Asian (EAS) AF: 0.760 AC: 3926 AN: 5166

South Asian (SAS) AF: 0.760 AC: 3661 AN: 4820

European-Finnish (FIN) AF: 0.553 AC: 5827 AN: 10528

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38836 AN: 67974

Other (OTH) AF: 0.616 AC: 1299 AN: 2108

Alfa AF: 0.574 Hom.: 36665

Bravo AF: 0.589

Asia WGS AF: 0.735 AC: 2551 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.032
DANN	Benign	0.42
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10188961; hg19: chr2-4926593;