8-81244318-C-T

Variant names:

• chr8-81244318-C-T
• rs9298347
• ENST00000519351.1:n.163C>T

Variant summary

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

The ENST00000519351.1(ENSG00000254014):​n.163C>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 0.451 in 152,070 control chromosomes in the GnomAD database, including 17,850 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 0.45 (17844 hom., cov: 32)
  • Exomes 𝑓: 0.38 (6 hom.)
• Consequence: ENSG00000254014 ENST00000519351.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615

Genes affected

ENSG00000254014 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.594 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
ENSG00000254014	ENST00000519351.1	n.163C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68627 AN: 151880 Hom.: 17851 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.476

GnomAD4 exome AF: 0.378 AC: 28 AN: 74 Hom.: 6 Cov.: 0 AF XY: 0.400 AC XY: 20 AN XY: 50

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.433

Gnomad4 NFE exome AF: 0.412

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.452 AC: 68629 AN: 151996 Hom.: 17844 Cov.: 32 AF XY: 0.443 AC XY: 32915 AN XY: 74278

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.0499

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.472

Alfa AF: 0.554 Hom.: 14916

Bravo AF: 0.425

Asia WGS AF: 0.201 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.75
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9298347; hg19: chr8-82156553;