8-13940496-C-T

Variant names:

• chr8-13940496-C-T
• rs2682665

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 0.922 in 152,194 control chromosomes in the GnomAD database, including 65,567 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 0.92 (65567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 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: 0.922 AC: 140274 AN: 152076 Hom.: 65537 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.975

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.922 AC: 140358 AN: 152194 Hom.: 65567 Cov.: 32 AF XY: 0.924 AC XY: 68735 AN XY: 74412

African (AFR) AF: 0.750 AC: 31139 AN: 41496

American (AMR) AF: 0.954 AC: 14580 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3277 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5147 AN: 5148

South Asian (SAS) AF: 0.975 AC: 4707 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10625 AN: 10626

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67737 AN: 68014

Other (OTH) AF: 0.925 AC: 1958 AN: 2116

Alfa AF: 0.968 Hom.: 201332

Bravo AF: 0.910

Asia WGS AF: 0.975 AC: 3390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.42
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs2682665; hg19: chr8-13798005;