rs10492555

Variant names:

• chr13-36134972-C-A
• rs10492555

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 0.189 in 152,118 control chromosomes in the GnomAD database, including 2,897 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 0.19 (2897 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.289 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: 0.189 AC: 28692 AN: 152000 Hom.: 2894 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.189 AC: 28707 AN: 152118 Hom.: 2897 Cov.: 32 AF XY: 0.192 AC XY: 14268 AN XY: 74354

African (AFR) AF: 0.232 AC: 9606 AN: 41476

American (AMR) AF: 0.166 AC: 2543 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3470

East Asian (EAS) AF: 0.284 AC: 1466 AN: 5154

South Asian (SAS) AF: 0.302 AC: 1450 AN: 4808

European-Finnish (FIN) AF: 0.170 AC: 1804 AN: 10584

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.154 AC: 10496 AN: 68012

Other (OTH) AF: 0.184 AC: 389 AN: 2116

Alfa AF: 0.167 Hom.: 6622

Bravo AF: 0.188

Asia WGS AF: 0.284 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10492555; hg19: chr13-36709109;