3-167031765-C-G

Variant names:

• chr3-167031765-C-G
• rs2030350

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 0.759 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.658 AC: 27254 AN: 41424

American (AMR) AF: 0.844 AC: 12848 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3005 AN: 3470

East Asian (EAS) AF: 0.845 AC: 4354 AN: 5152

South Asian (SAS) AF: 0.804 AC: 3862 AN: 4804

European-Finnish (FIN) AF: 0.732 AC: 7718 AN: 10546

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53621 AN: 67936

Other (OTH) AF: 0.796 AC: 1682 AN: 2112

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
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs2030350; hg19: chr3-166749553;