rs10492621

Variant names:

• chr13-93027812-G-A
• rs10492621

Your query was ambiguous. Multiple possible variants found:

• chr13-93027812-G-A
• chr13-93027812-G-C

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 0.173 in 151,882 control chromosomes in the GnomAD database, including 2,851 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 0.17 (2851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.669
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 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: 0.173 AC: 26311 AN: 151764 Hom.: 2848 Cov.: 32

Gnomad AFR AF: 0.0416

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.173 AC: 26312 AN: 151882 Hom.: 2851 Cov.: 32 AF XY: 0.174 AC XY: 12914 AN XY: 74206

African (AFR) AF: 0.0415 AC: 1722 AN: 41530

American (AMR) AF: 0.220 AC: 3354 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3470

East Asian (EAS) AF: 0.153 AC: 788 AN: 5158

South Asian (SAS) AF: 0.116 AC: 558 AN: 4816

European-Finnish (FIN) AF: 0.239 AC: 2521 AN: 10548

Middle Eastern (MID) AF: 0.234 AC: 68 AN: 290

European-Non Finnish (NFE) AF: 0.234 AC: 15894 AN: 67818

Other (OTH) AF: 0.184 AC: 388 AN: 2106

Alfa AF: 0.205 Hom.: 5287

Bravo AF: 0.168

Asia WGS AF: 0.107 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	8.2
DANN	Benign	0.84
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs10492621; hg19: chr13-93680065;