rs17483139

Variant names:

• chr15-49712315-A-G
• rs17483139

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 0.178 in 152,204 control chromosomes in the GnomAD database, including 2,987 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 0.18 (2987 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 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: 0.179 AC: 27161 AN: 152086 Hom.: 2988 Cov.: 33

Gnomad AFR AF: 0.0631

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.178 AC: 27158 AN: 152204 Hom.: 2987 Cov.: 33 AF XY: 0.181 AC XY: 13461 AN XY: 74412

Gnomad4 AFR AF: 0.0632

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.00462

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.193

Alfa AF: 0.206 Hom.: 579

Bravo AF: 0.162

Asia WGS AF: 0.0770 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17483139; hg19: chr15-50004512;