rs17483139

Variant names:

• chr15-49712315-A-G
• rs17483139

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0632 AC: 2627 AN: 41534

American (AMR) AF: 0.157 AC: 2403 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3470

East Asian (EAS) AF: 0.00462 AC: 24 AN: 5192

South Asian (SAS) AF: 0.171 AC: 823 AN: 4816

European-Finnish (FIN) AF: 0.313 AC: 3313 AN: 10588

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16445 AN: 67992

Other (OTH) AF: 0.193 AC: 407 AN: 2112

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs17483139; hg19: chr15-50004512;