3-166296681-G-C

Variant names:

• chr3-166296681-G-C
• rs509208

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.782

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs509208; hg19: chr3-166014469;