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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.673

Alfa AF: 0.640 Hom.: 62708

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513581; hg19: chr3-161939246;