3-162781846-G-C

Variant names:

• chr3-162781846-G-C
• rs206293

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 0.815 in 151,188 control chromosomes in the GnomAD database, including 50,637 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 0.81 (50637 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521
• Publications: 2 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 = 0.961 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: 0.815 AC: 123069 AN: 151072 Hom.: 50586 Cov.: 32

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.815 AC: 123179 AN: 151188 Hom.: 50637 Cov.: 32 AF XY: 0.818 AC XY: 60390 AN XY: 73808

African (AFR) AF: 0.914 AC: 37872 AN: 41452

American (AMR) AF: 0.836 AC: 12638 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2660 AN: 3468

East Asian (EAS) AF: 0.984 AC: 5069 AN: 5154

South Asian (SAS) AF: 0.864 AC: 4170 AN: 4826

European-Finnish (FIN) AF: 0.783 AC: 8134 AN: 10394

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.742 AC: 50038 AN: 67480

Other (OTH) AF: 0.814 AC: 1710 AN: 2102

Alfa AF: 0.668 Hom.: 1834

Bravo AF: 0.824

Asia WGS AF: 0.929 AC: 3211 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.31
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs206293; hg19: chr3-162499634;