ENST00000517626.1:n.-115G>T

Variant names:

• chr8-1730091-G-T
• rs12545625
• ENST00000517626.1:n.-115G>T

Variant summary

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

The ENST00000517626.1(ENSG00000254265):​n.-115G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,092 control chromosomes in the GnomAD database, including 4,463 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 0.24 (4463 hom., cov: 33)
  • Exomes 𝑓: 0.18 (0 hom.)
• Consequence: ENSG00000254265 ENST00000517626.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

Genes affected

ENSG00000254265 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 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
ENSG00000254265	ENST00000517626.1	n.-115G>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35888 AN: 151936 Hom.: 4462 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.230

GnomAD4 exome AF: 0.184 AC: 7 AN: 38 Hom.: 0 AF XY: 0.167 AC XY: 5 AN XY: 30

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.115

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.236 AC: 35914 AN: 152054 Hom.: 4463 Cov.: 33 AF XY: 0.237 AC XY: 17640 AN XY: 74336

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.228

Alfa AF: 0.249 Hom.: 2387

Bravo AF: 0.228

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12545625; hg19: chr8-1678257;