8-109083404-C-T

Variant names:

• chr8-109083404-C-T
• rs3110040

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 0.662 in 151,874 control chromosomes in the GnomAD database, including 33,859 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 0.66 (33859 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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: 0.662 AC: 100463 AN: 151754 Hom.: 33810 Cov.: 30

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.662 AC: 100584 AN: 151874 Hom.: 33859 Cov.: 30 AF XY: 0.666 AC XY: 49442 AN XY: 74198

African (AFR) AF: 0.770 AC: 31871 AN: 41414

American (AMR) AF: 0.735 AC: 11222 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1702 AN: 3468

East Asian (EAS) AF: 0.568 AC: 2907 AN: 5118

South Asian (SAS) AF: 0.729 AC: 3507 AN: 4808

European-Finnish (FIN) AF: 0.607 AC: 6405 AN: 10548

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40807 AN: 67938

Other (OTH) AF: 0.671 AC: 1414 AN: 2106

Alfa AF: 0.619 Hom.: 91758

Bravo AF: 0.674

Asia WGS AF: 0.691 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.86
DANN	Benign	0.63
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3110040; hg19: chr8-110095633;