17-14554683-C-T

Variant names:

• chr17-14554683-C-T
• rs1015767

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 0.548 in 151,942 control chromosomes in the GnomAD database, including 26,188 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 0.55 (26188 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83296 AN: 151824 Hom.: 26190 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.548 AC: 83312 AN: 151942 Hom.: 26188 Cov.: 31 AF XY: 0.552 AC XY: 40976 AN XY: 74234

African (AFR) AF: 0.219 AC: 9064 AN: 41414

American (AMR) AF: 0.569 AC: 8693 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2296 AN: 3470

East Asian (EAS) AF: 0.683 AC: 3515 AN: 5150

South Asian (SAS) AF: 0.793 AC: 3814 AN: 4810

European-Finnish (FIN) AF: 0.664 AC: 7017 AN: 10562

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46756 AN: 67946

Other (OTH) AF: 0.579 AC: 1223 AN: 2112

Alfa AF: 0.642 Hom.: 134552

Bravo AF: 0.524

Asia WGS AF: 0.701 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.55
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs1015767; hg19: chr17-14458000;