17-15193839-T-C

Variant names:

• chr17-15193839-T-C
• rs231008

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 0.747 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.747 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

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.727

Alfa AF: 0.736 Hom.: 6940

Bravo AF: 0.743

Asia WGS AF: 0.837 AC: 2912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs231008; hg19: chr17-15097156;