rs10509429

Variant names:

• chr10-81258462-G-A
• rs10509429

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 0.0363 in 152,228 control chromosomes in the GnomAD database, including 207 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 0.036 (207 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 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: 0.0360 AC: 5481 AN: 152110 Hom.: 202 Cov.: 32

Gnomad AFR AF: 0.0879

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.00990

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00676

Gnomad OTH AF: 0.0398

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

GnomAD4 genome AF: 0.0363 AC: 5519 AN: 152228 Hom.: 207 Cov.: 32 AF XY: 0.0367 AC XY: 2731 AN XY: 74436

African (AFR) AF: 0.0886 AC: 3677 AN: 41522

American (AMR) AF: 0.0170 AC: 260 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3472

East Asian (EAS) AF: 0.122 AC: 630 AN: 5168

South Asian (SAS) AF: 0.0354 AC: 171 AN: 4824

European-Finnish (FIN) AF: 0.00990 AC: 105 AN: 10608

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00676 AC: 460 AN: 68020

Other (OTH) AF: 0.0403 AC: 85 AN: 2110

Alfa AF: 0.0298 Hom.: 73

Bravo AF: 0.0393

Asia WGS AF: 0.0790 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.55
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10509429; hg19: chr10-83018218;