rs10492705

Variant names:

• chr13-57245317-T-C
• rs10492705

Your query was ambiguous. Multiple possible variants found:

• chr13-57245317-T-C
• chr13-57245317-T-G

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 0.136 in 150,848 control chromosomes in the GnomAD database, including 1,533 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 0.14 (1533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.291 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: 0.136 AC: 20495 AN: 150728 Hom.: 1528 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.136 AC: 20531 AN: 150848 Hom.: 1533 Cov.: 32 AF XY: 0.137 AC XY: 10121 AN XY: 73684

African (AFR) AF: 0.143 AC: 5896 AN: 41304

American (AMR) AF: 0.0940 AC: 1419 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 496 AN: 3448

East Asian (EAS) AF: 0.304 AC: 1543 AN: 5078

South Asian (SAS) AF: 0.140 AC: 676 AN: 4816

European-Finnish (FIN) AF: 0.149 AC: 1569 AN: 10564

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8292 AN: 67254

Other (OTH) AF: 0.141 AC: 294 AN: 2088

Alfa AF: 0.127 Hom.: 647

Bravo AF: 0.136

Asia WGS AF: 0.215 AC: 744 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.33
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10492705; hg19: chr13-57819451;