rs10510911

Variant names:

• chr3-63717965-C-G
• rs10510911

Your query was ambiguous. Multiple possible variants found:

• chr3-63717965-C-G
• chr3-63717965-C-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 0.387 in 151,988 control chromosomes in the GnomAD database, including 11,413 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 0.39 (11413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.397 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: 0.386 AC: 58689 AN: 151870 Hom.: 11391 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.387 AC: 58762 AN: 151988 Hom.: 11413 Cov.: 32 AF XY: 0.385 AC XY: 28613 AN XY: 74292

African (AFR) AF: 0.370 AC: 15344 AN: 41464

American (AMR) AF: 0.406 AC: 6187 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3466

East Asian (EAS) AF: 0.359 AC: 1855 AN: 5168

South Asian (SAS) AF: 0.288 AC: 1388 AN: 4812

European-Finnish (FIN) AF: 0.416 AC: 4401 AN: 10572

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.398 AC: 27046 AN: 67940

Other (OTH) AF: 0.396 AC: 834 AN: 2108

Alfa AF: 0.387 Hom.: 1609

Bravo AF: 0.388

Asia WGS AF: 0.351 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.38
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs10510911; hg19: chr3-63703641;