chr17-15214758-A-G

Position:

• chr17-15214758-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 0.783 in 151,964 control chromosomes in the GnomAD database, including 46,906 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 0.78 (46906 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 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: 0.783 AC: 118833 AN: 151846 Hom.: 46851 Cov.: 30

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.783 AC: 118944 AN: 151964 Hom.: 46906 Cov.: 30 AF XY: 0.784 AC XY: 58182 AN XY: 74252

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.769

Alfa AF: 0.724 Hom.: 15680

Bravo AF: 0.789

Asia WGS AF: 0.774 AC: 2688 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.039
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230926; hg19: chr17-15118075; COSMIC: COSV69373140;