3-167031765-C-G

Position:

• chr3-167031765-C-G

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 0.759 in 151,870 control chromosomes in the GnomAD database, including 44,080 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 0.76 (44080 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115242 AN: 151752 Hom.: 44060 Cov.: 30

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.759 AC: 115308 AN: 151870 Hom.: 44080 Cov.: 30 AF XY: 0.762 AC XY: 56545 AN XY: 74222

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.796

Alfa AF: 0.767 Hom.: 5264

Bravo AF: 0.762

Asia WGS AF: 0.807 AC: 2806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2030350; hg19: chr3-166749553;