8-138967582-A-T

Variant names:

• chr8-138967582-A-T
• rs4736192

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 0.21 in 152,116 control chromosomes in the GnomAD database, including 4,965 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 0.21 (4965 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 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: 0.210 AC: 31870 AN: 151998 Hom.: 4954 Cov.: 32

Gnomad AFR AF: 0.0667

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.210 AC: 31899 AN: 152116 Hom.: 4965 Cov.: 32 AF XY: 0.218 AC XY: 16198 AN XY: 74382

African (AFR) AF: 0.0668 AC: 2774 AN: 41552

American (AMR) AF: 0.398 AC: 6065 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 435 AN: 3470

East Asian (EAS) AF: 0.746 AC: 3838 AN: 5142

South Asian (SAS) AF: 0.361 AC: 1736 AN: 4814

European-Finnish (FIN) AF: 0.202 AC: 2139 AN: 10580

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14357 AN: 67986

Other (OTH) AF: 0.195 AC: 412 AN: 2114

Alfa AF: 0.107 Hom.: 175

Bravo AF: 0.219

Asia WGS AF: 0.511 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.67
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs4736192; hg19: chr8-139979825;