chr17-82450939-C-T

Position:

• chr17-82450939-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658363.1(ENSG00000287193):​n.29C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,028 control chromosomes in the GnomAD database, including 2,690 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 0.18 (2690 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000287193 ENST00000658363.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

Genes affected

ENSG00000287193 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.82450939C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287193	ENST00000658363.1	n.29C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26695 AN: 151912 Hom.: 2672 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.175

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.176 AC: 26772 AN: 152028 Hom.: 2690 Cov.: 32 AF XY: 0.181 AC XY: 13419 AN XY: 74328

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.180

Alfa AF: 0.129 Hom.: 1520

Bravo AF: 0.185

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.1
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: rs9303029; hg19: chr17-80408815;