ENST00000791453.1:n.290A>G

Variant names:

• chr13-76715842-A-G
• rs2149698
• ENST00000791453.1:n.290A>G

Variant summary

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

The ENST00000791453.1(ENSG00000287018):​n.290A>G 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 0.333 in 151,400 control chromosomes in the GnomAD database, including 10,605 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 0.33 (10605 hom., cov: 30)
• Consequence: ENSG00000287018 ENST00000791453.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 4 publications found

Genes affected

ENSG00000287018 (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 (AMR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791453.1. 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
	ENSG00000287018	ENST00000791453.1		n.290A>G		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000285572	ENST00000648060.1		n.395+13503T>C		intron	N/A
	ENSG00000285572	ENST00000791172.1		n.477-1087T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50483 AN: 151280 Hom.: 10599 Cov.: 30

Gnomad AFR AF: 0.0818

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.333 AC: 50485 AN: 151400 Hom.: 10605 Cov.: 30 AF XY: 0.338 AC XY: 24957 AN XY: 73938

African (AFR) AF: 0.0815 AC: 3373 AN: 41368

American (AMR) AF: 0.542 AC: 8233 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1459 AN: 3462

East Asian (EAS) AF: 0.478 AC: 2443 AN: 5116

South Asian (SAS) AF: 0.379 AC: 1815 AN: 4788

European-Finnish (FIN) AF: 0.390 AC: 4049 AN: 10386

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.410 AC: 27801 AN: 67790

Other (OTH) AF: 0.338 AC: 713 AN: 2108

Alfa AF: 0.397 Hom.: 21456

Bravo AF: 0.336

Asia WGS AF: 0.371 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.027
DANN	Benign	0.58
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2149698;

hg19: chr13-77289977;