chr8-130027263-T-A

Variant names:

• chr8-130027263-T-A
• rs10505546

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 0.453 in 151,764 control chromosomes in the GnomAD database, including 15,733 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 0.45 (15733 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 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 (AMR) allele frequency at 95% confidence interval = 0.49 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: 0.453 AC: 68687 AN: 151646 Hom.: 15712 Cov.: 31

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.453 AC: 68752 AN: 151764 Hom.: 15733 Cov.: 31 AF XY: 0.453 AC XY: 33523 AN XY: 74082

African (AFR) AF: 0.416 AC: 17225 AN: 41360

American (AMR) AF: 0.499 AC: 7608 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1546 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1908 AN: 5150

South Asian (SAS) AF: 0.360 AC: 1739 AN: 4824

European-Finnish (FIN) AF: 0.500 AC: 5218 AN: 10426

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.468 AC: 31825 AN: 67986

Other (OTH) AF: 0.439 AC: 925 AN: 2108

Alfa AF: 0.336 Hom.: 891

Bravo AF: 0.453

Asia WGS AF: 0.420 AC: 1459 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	0.67
DANN	Benign	0.35
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10505546; hg19: chr8-131039509;