3-148664618-G-A

Variant names:

• chr3-148664618-G-A
• rs903051

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 0.563 in 151,862 control chromosomes in the GnomAD database, including 25,336 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 0.56 (25336 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 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: 0.563 AC: 85403 AN: 151744 Hom.: 25315 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.563 AC: 85468 AN: 151862 Hom.: 25336 Cov.: 31 AF XY: 0.568 AC XY: 42179 AN XY: 74232

African (AFR) AF: 0.373 AC: 15441 AN: 41408

American (AMR) AF: 0.695 AC: 10601 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1893 AN: 3470

East Asian (EAS) AF: 0.810 AC: 4170 AN: 5146

South Asian (SAS) AF: 0.542 AC: 2602 AN: 4804

European-Finnish (FIN) AF: 0.675 AC: 7124 AN: 10552

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41836 AN: 67912

Other (OTH) AF: 0.559 AC: 1179 AN: 2108

Alfa AF: 0.583 Hom.: 4263

Bravo AF: 0.561

Asia WGS AF: 0.646 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.36
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs903051; hg19: chr3-148382405;