rs17483139

chr15-49712315-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 0.178 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;