ENST00000790899.1:n.-179C>T

Variant names:

• chr6-32690533-G-A
• rs9469220
• ENST00000790899.1:n.-179C>T

Variant summary

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

The ENST00000790899.1(ENSG00000302994):​n.-179C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,794 control chromosomes in the GnomAD database, including 21,624 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 0.53 (21624 hom., cov: 31)
• Consequence: ENSG00000302994 ENST00000790899.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 86 publications found

Genes affected

ENSG00000302994 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 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
ENSG00000302994	ENST00000790899.1	n.-179C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80536 AN: 151676 Hom.: 21609 Cov.: 31

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.531 AC: 80594 AN: 151794 Hom.: 21624 Cov.: 31 AF XY: 0.532 AC XY: 39429 AN XY: 74164

African (AFR) AF: 0.559 AC: 23121 AN: 41398

American (AMR) AF: 0.544 AC: 8300 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2053 AN: 3462

East Asian (EAS) AF: 0.654 AC: 3373 AN: 5154

South Asian (SAS) AF: 0.574 AC: 2758 AN: 4808

European-Finnish (FIN) AF: 0.511 AC: 5373 AN: 10514

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33656 AN: 67886

Other (OTH) AF: 0.578 AC: 1215 AN: 2102

Alfa AF: 0.502 Hom.: 67811

Bravo AF: 0.536

Asia WGS AF: 0.643 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.27
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9469220; hg19: chr6-32658310;