3-51882999-C-A

Variant names:

• chr3-51882999-C-A
• rs1605070

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 0.611 in 152,018 control chromosomes in the GnomAD database, including 29,681 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 0.61 (29681 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92781 AN: 151900 Hom.: 29672 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.611 AC: 92823 AN: 152018 Hom.: 29681 Cov.: 32 AF XY: 0.616 AC XY: 45770 AN XY: 74294

African (AFR) AF: 0.424 AC: 17561 AN: 41452

American (AMR) AF: 0.734 AC: 11210 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2059 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4767 AN: 5166

South Asian (SAS) AF: 0.735 AC: 3544 AN: 4822

European-Finnish (FIN) AF: 0.604 AC: 6370 AN: 10552

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45168 AN: 67962

Other (OTH) AF: 0.635 AC: 1339 AN: 2110

Alfa AF: 0.646 Hom.: 98672

Bravo AF: 0.607

Asia WGS AF: 0.798 AC: 2771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.43
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1605070; hg19: chr3-51917015;