10-130763689-C-T

Variant names:

• chr10-130763689-C-T
• rs10829792

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 0.496 in 151,724 control chromosomes in the GnomAD database, including 19,648 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 0.50 (19648 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 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: 0.496 AC: 75204 AN: 151604 Hom.: 19651 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.496 AC: 75210 AN: 151724 Hom.: 19648 Cov.: 31 AF XY: 0.493 AC XY: 36581 AN XY: 74162

African (AFR) AF: 0.323 AC: 13324 AN: 41262

American (AMR) AF: 0.555 AC: 8462 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1798 AN: 3464

East Asian (EAS) AF: 0.644 AC: 3312 AN: 5140

South Asian (SAS) AF: 0.487 AC: 2339 AN: 4806

European-Finnish (FIN) AF: 0.516 AC: 5449 AN: 10564

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38721 AN: 67938

Other (OTH) AF: 0.479 AC: 1008 AN: 2106

Alfa AF: 0.539 Hom.: 69473

Bravo AF: 0.493

Asia WGS AF: 0.497 AC: 1729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.51
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10829792; hg19: chr10-132561953;