10-81330792-C-T

Variant names:

• chr10-81330792-C-T
• rs10509433

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 0.114 in 152,032 control chromosomes in the GnomAD database, including 1,738 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 0.11 (1738 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.491 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: 0.114 AC: 17357 AN: 151914 Hom.: 1735 Cov.: 32

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.114 AC: 17386 AN: 152032 Hom.: 1738 Cov.: 32 AF XY: 0.122 AC XY: 9067 AN XY: 74318

African (AFR) AF: 0.0970 AC: 4025 AN: 41486

American (AMR) AF: 0.201 AC: 3065 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3472

East Asian (EAS) AF: 0.508 AC: 2622 AN: 5166

South Asian (SAS) AF: 0.318 AC: 1531 AN: 4808

European-Finnish (FIN) AF: 0.103 AC: 1091 AN: 10568

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0686 AC: 4660 AN: 67962

Other (OTH) AF: 0.107 AC: 224 AN: 2102

Alfa AF: 0.0851 Hom.: 3757

Bravo AF: 0.122

Asia WGS AF: 0.365 AC: 1265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.25
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs10509433; hg19: chr10-83090548;