chr8-131559152-T-C

Variant names:

• chr8-131559152-T-C
• rs277001

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 0.557 in 151,960 control chromosomes in the GnomAD database, including 25,209 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 (25209 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84518 AN: 151838 Hom.: 25171 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.557 AC: 84600 AN: 151960 Hom.: 25209 Cov.: 31 AF XY: 0.548 AC XY: 40679 AN XY: 74276

African (AFR) AF: 0.768 AC: 31841 AN: 41476

American (AMR) AF: 0.405 AC: 6173 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1166 AN: 5152

South Asian (SAS) AF: 0.361 AC: 1739 AN: 4820

European-Finnish (FIN) AF: 0.496 AC: 5215 AN: 10524

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35066 AN: 67950

Other (OTH) AF: 0.491 AC: 1035 AN: 2108

Alfa AF: 0.534 Hom.: 2650

Bravo AF: 0.556

Asia WGS AF: 0.298 AC: 1038 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.26
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs277001; hg19: chr8-132571399; COSMIC: COSV64449860;