ENST00000793953.1:n.-213G>A

Variant names:

• chr8-79726489-C-T
• rs11997947
• ENST00000793953.1:n.-213G>A

Variant summary

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

The ENST00000793953.1(ENSG00000303364):​n.-213G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0595 in 152,244 control chromosomes in the GnomAD database, including 284 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 0.059 (284 hom., cov: 32)
• Consequence: ENSG00000303364 ENST00000793953.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 1 publications found

Genes affected

ENSG00000303364 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793953.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303364	ENST00000793953.1		n.-213G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0593 AC: 9028 AN: 152126 Hom.: 280 Cov.: 32

Gnomad AFR AF: 0.0709

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0291

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0588

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0595 AC: 9051 AN: 152244 Hom.: 284 Cov.: 32 AF XY: 0.0589 AC XY: 4387 AN XY: 74430

African (AFR) AF: 0.0714 AC: 2963 AN: 41522

American (AMR) AF: 0.0290 AC: 443 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3472

East Asian (EAS) AF: 0.0526 AC: 273 AN: 5192

South Asian (SAS) AF: 0.0485 AC: 234 AN: 4826

European-Finnish (FIN) AF: 0.0753 AC: 798 AN: 10594

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0588 AC: 4001 AN: 68020

Other (OTH) AF: 0.0614 AC: 130 AN: 2116

Alfa AF: 0.0558 Hom.: 367

Bravo AF: 0.0562

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.41
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs11997947; hg19: chr8-80638724;