17-15350248-G-A

Position:

• chr17-15350248-G-A

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 0.0501 in 152,100 control chromosomes in the GnomAD database, including 324 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 0.050 (324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0501 AC: 7620 AN: 151982 Hom.: 325 Cov.: 32

Gnomad AFR AF: 0.0121

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0389

Gnomad ASJ AF: 0.0586

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.0532

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

GnomAD4 genome AF: 0.0501 AC: 7614 AN: 152100 Hom.: 324 Cov.: 32 AF XY: 0.0523 AC XY: 3888 AN XY: 74348

Gnomad4 AFR AF: 0.0120

Gnomad4 AMR AF: 0.0389

Gnomad4 ASJ AF: 0.0586

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0548

Gnomad4 NFE AF: 0.0575

Gnomad4 OTH AF: 0.0512

Alfa AF: 0.0578 Hom.: 377

Bravo AF: 0.0473

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12937472; hg19: chr17-15253565;