rs10885493

Variant names:

• chr10-113671174-G-A
• rs10885493

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 0.0999 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
• 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 (NFE) allele frequency at 95% confidence interval = 0.13 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: 0.100 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

African (AFR) AF: 0.0491 AC: 2039 AN: 41512

American (AMR) AF: 0.0987 AC: 1511 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3472

East Asian (EAS) AF: 0.0294 AC: 152 AN: 5178

South Asian (SAS) AF: 0.0504 AC: 243 AN: 4822

European-Finnish (FIN) AF: 0.146 AC: 1543 AN: 10590

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8978 AN: 68000

Other (OTH) AF: 0.0922 AC: 195 AN: 2114

Alfa AF: 0.115 Hom.: 2947

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10885493; hg19: chr10-115430933;