rs10510126

Variant names:

• chr10-123242969-C-T
• rs10510126

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 0.116 in 152,228 control chromosomes in the GnomAD database, including 1,118 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 0.12 (1118 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.131 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: 0.116 AC: 17657 AN: 152110 Hom.: 1122 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0583

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.116 AC: 17664 AN: 152228 Hom.: 1118 Cov.: 33 AF XY: 0.119 AC XY: 8856 AN XY: 74434

African (AFR) AF: 0.108 AC: 4502 AN: 41534

American (AMR) AF: 0.136 AC: 2075 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 371 AN: 3472

East Asian (EAS) AF: 0.0583 AC: 302 AN: 5184

South Asian (SAS) AF: 0.138 AC: 665 AN: 4814

European-Finnish (FIN) AF: 0.147 AC: 1559 AN: 10594

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7681 AN: 68018

Other (OTH) AF: 0.125 AC: 264 AN: 2112

Alfa AF: 0.116 Hom.: 1475

Bravo AF: 0.113

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.56
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs10510126; hg19: chr10-125002485;