chr15-50373165-A-T

Variant names:

• chr15-50373165-A-T
• rs17509458

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 0.266 in 151,710 control chromosomes in the GnomAD database, including 6,832 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 0.27 (6832 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 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: 0.266 AC: 40387 AN: 151590 Hom.: 6833 Cov.: 31

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.00852

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.266 AC: 40395 AN: 151710 Hom.: 6832 Cov.: 31 AF XY: 0.260 AC XY: 19273 AN XY: 74114

African (AFR) AF: 0.0888 AC: 3675 AN: 41362

American (AMR) AF: 0.348 AC: 5306 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1013 AN: 3470

East Asian (EAS) AF: 0.00854 AC: 44 AN: 5154

South Asian (SAS) AF: 0.283 AC: 1361 AN: 4806

European-Finnish (FIN) AF: 0.222 AC: 2331 AN: 10478

Middle Eastern (MID) AF: 0.428 AC: 124 AN: 290

European-Non Finnish (NFE) AF: 0.375 AC: 25468 AN: 67896

Other (OTH) AF: 0.288 AC: 606 AN: 2102

Alfa AF: 0.296 Hom.: 962

Bravo AF: 0.270

Asia WGS AF: 0.134 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.52
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17509458; hg19: chr15-50665362;