rs17086849

Variant names:

• chr13-28592262-G-A
• rs17086849

Your query was ambiguous. Multiple possible variants found:

• chr13-28592262-G-A
• chr13-28592262-G-T

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 0.251 in 151,226 control chromosomes in the GnomAD database, including 5,348 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 0.25 (5348 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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: 0.251 AC: 37979 AN: 151106 Hom.: 5347 Cov.: 28

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.251 AC: 38019 AN: 151226 Hom.: 5348 Cov.: 28 AF XY: 0.252 AC XY: 18640 AN XY: 73850

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.229

Alfa AF: 0.196 Hom.: 1782

Bravo AF: 0.269

Asia WGS AF: 0.310 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17086849; hg19: chr13-29166399;