8-81244318-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000254014 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519351.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254014	ENST00000519351.1	TSL:6	n.163C>T		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.433 AC: 13 AN: 30

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.412 AC: 14 AN: 34

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.248 AC: 10265 AN: 41442

American (AMR) AF: 0.379 AC: 5791 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3468

East Asian (EAS) AF: 0.0499 AC: 257 AN: 5152

South Asian (SAS) AF: 0.372 AC: 1791 AN: 4812

European-Finnish (FIN) AF: 0.561 AC: 5928 AN: 10564

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40699 AN: 67966

Other (OTH) AF: 0.472 AC: 994 AN: 2108

Alfa AF: 0.549 Hom.: 17192

Bravo AF: 0.425

Asia WGS AF: 0.201 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.75
DANN	Benign	0.71
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs9298347; hg19: chr8-82156553;