rs684846

Variant names:

• chr3-183173176-C-T
• rs684846

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 0.851 in 152,140 control chromosomes in the GnomAD database, including 55,426 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 0.85 (55426 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129458 AN: 152022 Hom.: 55400 Cov.: 31

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.851 AC: 129530 AN: 152140 Hom.: 55426 Cov.: 31 AF XY: 0.851 AC XY: 63293 AN XY: 74382

African (AFR) AF: 0.756 AC: 31339 AN: 41464

American (AMR) AF: 0.858 AC: 13111 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3246 AN: 3472

East Asian (EAS) AF: 0.892 AC: 4613 AN: 5170

South Asian (SAS) AF: 0.813 AC: 3928 AN: 4830

European-Finnish (FIN) AF: 0.915 AC: 9687 AN: 10590

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60674 AN: 68020

Other (OTH) AF: 0.869 AC: 1838 AN: 2114

Alfa AF: 0.864 Hom.: 20177

Bravo AF: 0.844

Asia WGS AF: 0.863 AC: 3000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs684846; hg19: chr3-182890964;