rs17086849

Positions:

• 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.28592262G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;