rs10513713

Variant names:

• chr3-173361222-G-A
• rs10513713

Your query was ambiguous. Multiple possible variants found:

• chr3-173361222-G-A
• chr3-173361222-G-C

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 0.285 in 151,676 control chromosomes in the GnomAD database, including 7,179 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 0.28 (7179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 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: 0.285 AC: 43167 AN: 151558 Hom.: 7162 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.285 AC: 43227 AN: 151676 Hom.: 7179 Cov.: 32 AF XY: 0.287 AC XY: 21286 AN XY: 74142

African (AFR) AF: 0.440 AC: 18222 AN: 41386

American (AMR) AF: 0.253 AC: 3832 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 678 AN: 3466

East Asian (EAS) AF: 0.484 AC: 2486 AN: 5132

South Asian (SAS) AF: 0.348 AC: 1673 AN: 4808

European-Finnish (FIN) AF: 0.241 AC: 2547 AN: 10580

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12955 AN: 67818

Other (OTH) AF: 0.247 AC: 520 AN: 2104

Alfa AF: 0.218 Hom.: 15738

Bravo AF: 0.291

Asia WGS AF: 0.447 AC: 1551 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.24
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs10513713; hg19: chr3-173079012;