10-36582968-T-G

Variant names:

• chr10-36582968-T-G
• rs2151173

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 0.854 in 152,028 control chromosomes in the GnomAD database, including 55,704 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 0.85 (55704 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 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: 0.854 AC: 129790 AN: 151910 Hom.: 55672 Cov.: 30

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.854 AC: 129871 AN: 152028 Hom.: 55704 Cov.: 30 AF XY: 0.856 AC XY: 63609 AN XY: 74324

African (AFR) AF: 0.800 AC: 33156 AN: 41438

American (AMR) AF: 0.807 AC: 12333 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2912 AN: 3472

East Asian (EAS) AF: 0.787 AC: 4041 AN: 5136

South Asian (SAS) AF: 0.855 AC: 4117 AN: 4814

European-Finnish (FIN) AF: 0.928 AC: 9825 AN: 10586

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60603 AN: 67992

Other (OTH) AF: 0.834 AC: 1759 AN: 2110

Alfa AF: 0.883 Hom.: 34840

Bravo AF: 0.838

Asia WGS AF: 0.809 AC: 2812 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	1.4
DANN	Benign	0.37
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs2151173; hg19: chr10-36871896;