rs4686760

Variant names:

• chr3-184796825-G-A
• rs4686760

Your query was ambiguous. Multiple possible variants found:

• chr3-184796825-G-A
• chr3-184796825-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 0.425 in 151,898 control chromosomes in the GnomAD database, including 14,985 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 0.43 (14985 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 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: 0.426 AC: 64602 AN: 151780 Hom.: 14981 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.425 AC: 64614 AN: 151898 Hom.: 14985 Cov.: 31 AF XY: 0.422 AC XY: 31309 AN XY: 74228

African (AFR) AF: 0.239 AC: 9907 AN: 41396

American (AMR) AF: 0.525 AC: 8018 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1747 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1574 AN: 5154

South Asian (SAS) AF: 0.430 AC: 2074 AN: 4818

European-Finnish (FIN) AF: 0.384 AC: 4046 AN: 10548

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35835 AN: 67922

Other (OTH) AF: 0.458 AC: 965 AN: 2106

Alfa AF: 0.495 Hom.: 48097

Bravo AF: 0.428

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0050
DANN	Benign	0.71
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs4686760; hg19: chr3-184514613; COSMIC: COSV63001880;