3-23152437-G-A

Variant names:

• chr3-23152437-G-A
• rs4619807

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 0.766 in 152,018 control chromosomes in the GnomAD database, including 45,588 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 0.77 (45588 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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: 0.766 AC: 116385 AN: 151900 Hom.: 45513 Cov.: 31

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.766 AC: 116518 AN: 152018 Hom.: 45588 Cov.: 31 AF XY: 0.770 AC XY: 57190 AN XY: 74288

African (AFR) AF: 0.934 AC: 38752 AN: 41478

American (AMR) AF: 0.766 AC: 11702 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1935 AN: 3470

East Asian (EAS) AF: 0.821 AC: 4241 AN: 5168

South Asian (SAS) AF: 0.738 AC: 3559 AN: 4822

European-Finnish (FIN) AF: 0.733 AC: 7727 AN: 10548

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.678 AC: 46078 AN: 67950

Other (OTH) AF: 0.731 AC: 1538 AN: 2104

Alfa AF: 0.700 Hom.: 64142

Bravo AF: 0.778

Asia WGS AF: 0.818 AC: 2845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.30
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs4619807; hg19: chr3-23193928;