rs10509429

chr10-81258462-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;