10-117902581-T-C

Variant names:

• chr10-117902581-T-C
• rs1936295

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 0.832 in 152,070 control chromosomes in the GnomAD database, including 52,622 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 0.83 (52622 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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: 0.832 AC: 126369 AN: 151952 Hom.: 52584 Cov.: 30

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.832 AC: 126456 AN: 152070 Hom.: 52622 Cov.: 30 AF XY: 0.836 AC XY: 62152 AN XY: 74312

African (AFR) AF: 0.809 AC: 33546 AN: 41456

American (AMR) AF: 0.837 AC: 12793 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2779 AN: 3470

East Asian (EAS) AF: 0.947 AC: 4887 AN: 5162

South Asian (SAS) AF: 0.861 AC: 4127 AN: 4792

European-Finnish (FIN) AF: 0.885 AC: 9376 AN: 10592

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56199 AN: 68000

Other (OTH) AF: 0.825 AC: 1739 AN: 2108

Alfa AF: 0.821 Hom.: 64951

Bravo AF: 0.828

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.053
DANN	Benign	0.20
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1936295; hg19: chr10-119662092;