rs3776082

Variant names:

• chr5-150164482-G-A
• rs3776082

Your query was ambiguous. Multiple possible variants found:

• chr5-150164482-G-A
• chr5-150164482-G-C
• chr5-150164482-G-T

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 0.482 in 151,816 control chromosomes in the GnomAD database, including 17,954 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 0.48 (17954 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73124 AN: 151698 Hom.: 17930 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.482 AC: 73189 AN: 151816 Hom.: 17954 Cov.: 31 AF XY: 0.479 AC XY: 35542 AN XY: 74192

African (AFR) AF: 0.563 AC: 23304 AN: 41378

American (AMR) AF: 0.438 AC: 6679 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2173 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2833 AN: 5150

South Asian (SAS) AF: 0.477 AC: 2285 AN: 4794

European-Finnish (FIN) AF: 0.377 AC: 3966 AN: 10520

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30172 AN: 67922

Other (OTH) AF: 0.508 AC: 1073 AN: 2112

Alfa AF: 0.458 Hom.: 26469

Bravo AF: 0.488

Asia WGS AF: 0.505 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.46
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs3776082; hg19: chr5-149544045;