rs10492586

Variant names:

• chr13-104733738-A-G
• rs10492586

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 0.134 in 152,068 control chromosomes in the GnomAD database, including 2,520 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 0.13 (2520 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20391 AN: 151950 Hom.: 2517 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0959

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0726

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.0290

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.134 AC: 20416 AN: 152068 Hom.: 2520 Cov.: 32 AF XY: 0.135 AC XY: 10041 AN XY: 74350

African (AFR) AF: 0.322 AC: 13325 AN: 41432

American (AMR) AF: 0.0958 AC: 1460 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3470

East Asian (EAS) AF: 0.0722 AC: 373 AN: 5168

South Asian (SAS) AF: 0.213 AC: 1026 AN: 4818

European-Finnish (FIN) AF: 0.0290 AC: 308 AN: 10616

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0463 AC: 3147 AN: 68000

Other (OTH) AF: 0.134 AC: 283 AN: 2110

Alfa AF: 0.101 Hom.: 203

Bravo AF: 0.142

Asia WGS AF: 0.138 AC: 481 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.69
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs10492586; hg19: chr13-105386089;