rs10513581

Variant names:

• chr3-162221458-A-C
• rs10513581

Your query was ambiguous. Multiple possible variants found:

• chr3-162221458-A-C
• chr3-162221458-A-G
• chr3-162221458-A-T

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 0.655 in 151,766 control chromosomes in the GnomAD database, including 32,696 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 0.65 (32696 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99284 AN: 151648 Hom.: 32658 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.655 AC: 99384 AN: 151766 Hom.: 32696 Cov.: 31 AF XY: 0.651 AC XY: 48272 AN XY: 74182

African (AFR) AF: 0.719 AC: 29791 AN: 41424

American (AMR) AF: 0.651 AC: 9915 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2483 AN: 3466

East Asian (EAS) AF: 0.613 AC: 3132 AN: 5106

South Asian (SAS) AF: 0.535 AC: 2585 AN: 4828

European-Finnish (FIN) AF: 0.577 AC: 6086 AN: 10556

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43102 AN: 67846

Other (OTH) AF: 0.673 AC: 1424 AN: 2116

Alfa AF: 0.641 Hom.: 132532

Bravo AF: 0.666

Asia WGS AF: 0.627 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.38
DANN	Benign	0.81
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10513581; hg19: chr3-161939246;