3-166296681-G-C

Variant names:

• chr3-166296681-G-C
• rs509208

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 0.793 in 151,980 control chromosomes in the GnomAD database, including 48,314 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 0.79 (48314 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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: 0.793 AC: 120446 AN: 151862 Hom.: 48274 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.793 AC: 120535 AN: 151980 Hom.: 48314 Cov.: 31 AF XY: 0.795 AC XY: 59044 AN XY: 74300

African (AFR) AF: 0.661 AC: 27412 AN: 41440

American (AMR) AF: 0.861 AC: 13124 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2898 AN: 3470

East Asian (EAS) AF: 0.972 AC: 5006 AN: 5150

South Asian (SAS) AF: 0.872 AC: 4203 AN: 4822

European-Finnish (FIN) AF: 0.797 AC: 8417 AN: 10558

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56924 AN: 67982

Other (OTH) AF: 0.782 AC: 1651 AN: 2112

Alfa AF: 0.774 Hom.: 2477

Bravo AF: 0.792

Asia WGS AF: 0.895 AC: 3114 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	0.056
DANN	Benign	0.37
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs509208; hg19: chr3-166014469;