17-15214758-A-G

Variant names:

• chr17-15214758-A-G
• rs230926

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 0.783 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.880 AC: 36472 AN: 41460

American (AMR) AF: 0.801 AC: 12224 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2447 AN: 3470

East Asian (EAS) AF: 0.826 AC: 4254 AN: 5152

South Asian (SAS) AF: 0.707 AC: 3401 AN: 4808

European-Finnish (FIN) AF: 0.785 AC: 8277 AN: 10544

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49423 AN: 67950

Other (OTH) AF: 0.769 AC: 1621 AN: 2108

Alfa AF: 0.728 Hom.: 18064

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
PhyloP100		-3.5

Splicing

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

Other links and lift over

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