rs10509429

Variant names:

• chr10-81258462-G-A
• rs10509429

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 0.0363 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0886

Gnomad4 AMR AF: 0.0170

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.00990

Gnomad4 NFE AF: 0.00676

Gnomad4 OTH AF: 0.0403

Alfa AF: 0.0273 Hom.: 28

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509429; hg19: chr10-83018218;