17-50634726-C-T

Position:

• chr17-50634726-C-T

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 0.592 in 415,796 control chromosomes in the GnomAD database, including 74,465 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 0.59 (26632 hom., cov: 34)
  • Exomes 𝑓: 0.60 (47833 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50634726C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89329 AN: 151988 Hom.: 26603 Cov.: 34

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.589

GnomAD4 exome AF: 0.595 AC: 156957 AN: 263692 Hom.: 47833 AF XY: 0.593 AC XY: 78926 AN XY: 133082

Gnomad4 AFR exome AF: 0.581

Gnomad4 AMR exome AF: 0.624

Gnomad4 ASJ exome AF: 0.499

Gnomad4 EAS exome AF: 0.887

Gnomad4 SAS exome AF: 0.715

Gnomad4 FIN exome AF: 0.620

Gnomad4 NFE exome AF: 0.561

Gnomad4 OTH exome AF: 0.603

GnomAD4 genome AF: 0.588 AC: 89402 AN: 152104 Hom.: 26632 Cov.: 34 AF XY: 0.596 AC XY: 44294 AN XY: 74366

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.583

Alfa AF: 0.428 Hom.: 1097

Bravo AF: 0.589

Asia WGS AF: 0.721 AC: 2508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4793665; hg19: chr17-48712087; COSMIC: COSV53328058;