chr17-15193839-T-C

Variant names:

• chr17-15193839-T-C
• rs231008

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 0.747 in 151,994 control chromosomes in the GnomAD database, including 42,515 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 0.75 (42515 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.834 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: 0.747 AC: 113405 AN: 151876 Hom.: 42462 Cov.: 30

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.747 AC: 113517 AN: 151994 Hom.: 42515 Cov.: 30 AF XY: 0.750 AC XY: 55690 AN XY: 74282

African (AFR) AF: 0.751 AC: 31149 AN: 41452

American (AMR) AF: 0.721 AC: 11012 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2515 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4246 AN: 5136

South Asian (SAS) AF: 0.856 AC: 4120 AN: 4812

European-Finnish (FIN) AF: 0.744 AC: 7857 AN: 10562

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50267 AN: 67976

Other (OTH) AF: 0.727 AC: 1533 AN: 2110

Alfa AF: 0.736 Hom.: 7160

Bravo AF: 0.743

Asia WGS AF: 0.837 AC: 2912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.49
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs231008; hg19: chr17-15097156;