17-15193839-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;