rs13157690

Positions:

• chr5-10836373-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.482

Alfa AF: 0.558 Hom.: 21590

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13157690; hg19: chr5-10836485;