17-13018328-T-C

Position:

• chr17-13018328-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.729 in 289,472 control chromosomes in the GnomAD database, including 78,235 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.71 (39008 hom., cov: 34)
  • Exomes 𝑓: 0.75 (39227 hom.)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.892

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 17-13018328-T-C is Benign according to our data. Variant chr17-13018328-T-C is described in ClinVar as [Benign]. Clinvar id is 683498.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.13018328T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.710 AC: 108025 AN: 152054 Hom.: 39009 Cov.: 34

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.733

GnomAD4 exome AF: 0.749 AC: 102843 AN: 137300 Hom.: 39227 AF XY: 0.744 AC XY: 52452 AN XY: 70510

Gnomad4 AFR exome AF: 0.549

Gnomad4 AMR exome AF: 0.769

Gnomad4 ASJ exome AF: 0.788

Gnomad4 EAS exome AF: 0.885

Gnomad4 SAS exome AF: 0.674

Gnomad4 FIN exome AF: 0.785

Gnomad4 NFE exome AF: 0.749

Gnomad4 OTH exome AF: 0.751

GnomAD4 genome AF: 0.710 AC: 108064 AN: 152172 Hom.: 39008 Cov.: 34 AF XY: 0.714 AC XY: 53084 AN XY: 74392

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.733

Alfa AF: 0.745 Hom.: 20354

Bravo AF: 0.705

Asia WGS AF: 0.776 AC: 2701 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2051974; hg19: chr17-12921645;