3-161794785-A-G

Variant names:

• chr3-161794785-A-G
• rs10513572

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 0.516 in 152,032 control chromosomes in the GnomAD database, including 20,811 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 0.52 (20811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 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: 0.516 AC: 78356 AN: 151914 Hom.: 20784 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.516 AC: 78414 AN: 152032 Hom.: 20811 Cov.: 32 AF XY: 0.521 AC XY: 38745 AN XY: 74308

African (AFR) AF: 0.479 AC: 19871 AN: 41456

American (AMR) AF: 0.540 AC: 8261 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1660 AN: 3468

East Asian (EAS) AF: 0.912 AC: 4705 AN: 5158

South Asian (SAS) AF: 0.572 AC: 2758 AN: 4818

European-Finnish (FIN) AF: 0.551 AC: 5819 AN: 10568

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33736 AN: 67964

Other (OTH) AF: 0.500 AC: 1054 AN: 2110

Alfa AF: 0.488 Hom.: 11545

Bravo AF: 0.519

Asia WGS AF: 0.738 AC: 2563 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	1.3
DANN	Benign	0.29
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs10513572; hg19: chr3-161512573;