rs10764775

Variant names:

• chr10-128435544-T-C
• rs10764775

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.407

Alfa AF: 0.347 Hom.: 12572

Bravo AF: 0.421

Asia WGS AF: 0.577 AC: 2008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.066
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10764775; hg19: chr10-130233808;