ENST00000751533.1:n.-139G>A

Variant names:

• chr18-10078074-G-A
• rs8089099
• ENST00000751533.1:n.-139G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000751533.1(ENSG00000265554):​n.-139G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,148 control chromosomes in the GnomAD database, including 4,112 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 0.23 (4112 hom., cov: 33)
• Consequence: ENSG00000265554 ENST00000751533.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 9 publications found

Genes affected

ENSG00000265554 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 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
ENSG00000265554	ENST00000751533.1	n.-139G>A		upstream_gene_variant
ENSG00000265554	ENST00000751534.1	n.-150G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34334 AN: 152030 Hom.: 4113 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.236

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.226 AC: 34344 AN: 152148 Hom.: 4112 Cov.: 33 AF XY: 0.225 AC XY: 16719 AN XY: 74384

African (AFR) AF: 0.135 AC: 5618 AN: 41522

American (AMR) AF: 0.251 AC: 3840 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 807 AN: 3472

East Asian (EAS) AF: 0.287 AC: 1484 AN: 5176

South Asian (SAS) AF: 0.179 AC: 865 AN: 4822

European-Finnish (FIN) AF: 0.245 AC: 2594 AN: 10580

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18243 AN: 67966

Other (OTH) AF: 0.235 AC: 496 AN: 2112

Alfa AF: 0.254 Hom.: 15590

Bravo AF: 0.225

Asia WGS AF: 0.223 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.40
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs8089099; hg19: chr18-10078071;