rs10885493

chr10-113671174-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 0.0999 in 152,204 control chromosomes in the GnomAD database, including 917 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 0.10 (917 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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 (NFE) allele frequency at 95% confidence interval = 0.13 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: 0.100 AC: 15205 AN: 152086 Hom.: 917 Cov.: 32

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0295

Gnomad SAS AF: 0.0508

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0999 AC: 15198 AN: 152204 Hom.: 917 Cov.: 32 AF XY: 0.0987 AC XY: 7344 AN XY: 74410

Gnomad4 AFR AF: 0.0491

Gnomad4 AMR AF: 0.0987

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0294

Gnomad4 SAS AF: 0.0504

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.0922

Alfa AF: 0.120 Hom.: 1193

Bravo AF: 0.0947

Asia WGS AF: 0.0470 AC: 162 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	0.34
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10885493; hg19: chr10-115430933;