rs10829529

Variant names:

• chr10-128962085-C-T
• rs10829529

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 0.119 in 152,254 control chromosomes in the GnomAD database, including 1,333 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 (1333 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 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: 0.119 AC: 18078 AN: 152136 Hom.: 1332 Cov.: 33

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.119 AC: 18095 AN: 152254 Hom.: 1333 Cov.: 33 AF XY: 0.119 AC XY: 8827 AN XY: 74440

Gnomad4 AFR AF: 0.0348

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.126

Alfa AF: 0.123 Hom.: 159

Bravo AF: 0.117

Asia WGS AF: 0.171 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.94
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10829529; hg19: chr10-130760349; COSMIC: COSV71668545;