rs13157690

Variant names:

• chr5-10836373-A-G
• rs13157690

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 0.517 in 151,990 control chromosomes in the GnomAD database, including 20,798 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 0.52 (20798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 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: 0.517 AC: 78484 AN: 151872 Hom.: 20775 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.517 AC: 78553 AN: 151990 Hom.: 20798 Cov.: 32 AF XY: 0.513 AC XY: 38084 AN XY: 74286

African (AFR) AF: 0.481 AC: 19952 AN: 41450

American (AMR) AF: 0.536 AC: 8188 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2037 AN: 3468

East Asian (EAS) AF: 0.167 AC: 867 AN: 5180

South Asian (SAS) AF: 0.437 AC: 2108 AN: 4820

European-Finnish (FIN) AF: 0.506 AC: 5341 AN: 10548

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38398 AN: 67946

Other (OTH) AF: 0.482 AC: 1016 AN: 2108

Alfa AF: 0.553 Hom.: 28355

Bravo AF: 0.515

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs13157690; hg19: chr5-10836485;