rs10764775

Variant names:

• chr10-128435544-T-C
• rs10764775

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 0.413 in 152,086 control chromosomes in the GnomAD database, including 13,782 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 0.41 (13782 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.68
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.662 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: 0.413 AC: 62732 AN: 151968 Hom.: 13768 Cov.: 33

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.413 AC: 62788 AN: 152086 Hom.: 13782 Cov.: 33 AF XY: 0.417 AC XY: 30983 AN XY: 74368

African (AFR) AF: 0.536 AC: 22207 AN: 41452

American (AMR) AF: 0.384 AC: 5865 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3528 AN: 5182

South Asian (SAS) AF: 0.507 AC: 2445 AN: 4818

European-Finnish (FIN) AF: 0.348 AC: 3682 AN: 10580

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22525 AN: 67980

Other (OTH) AF: 0.407 AC: 859 AN: 2108

Alfa AF: 0.360 Hom.: 31032

Bravo AF: 0.421

Asia WGS AF: 0.577 AC: 2008 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	0.066
DANN	Benign	0.45
PhyloP100		-4.7

Splicing

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

Other links and lift over

dbSNP: rs10764775; hg19: chr10-130233808;