10-117228159-G-T

Variant names:

• chr10-117228159-G-T
• rs2532798

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 0.572 in 151,854 control chromosomes in the GnomAD database, including 27,843 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 0.57 (27843 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 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: 0.573 AC: 86927 AN: 151736 Hom.: 27841 Cov.: 30

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.572 AC: 86927 AN: 151854 Hom.: 27843 Cov.: 30 AF XY: 0.576 AC XY: 42769 AN XY: 74232

African (AFR) AF: 0.300 AC: 12408 AN: 41378

American (AMR) AF: 0.622 AC: 9492 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2618 AN: 3466

East Asian (EAS) AF: 0.213 AC: 1097 AN: 5144

South Asian (SAS) AF: 0.594 AC: 2859 AN: 4816

European-Finnish (FIN) AF: 0.780 AC: 8252 AN: 10578

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48218 AN: 67896

Other (OTH) AF: 0.601 AC: 1266 AN: 2106

Alfa AF: 0.667 Hom.: 54518

Bravo AF: 0.543

Asia WGS AF: 0.379 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.53
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2532798; hg19: chr10-118987670;