ENST00000790297.1:n.60G>T

Variant names:

• chr2-15642347-G-T
• rs807624
• ENST00000790297.1:n.60G>T

Variant summary

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

The ENST00000790297.1(ENSG00000302890):​n.60G>T 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 0.469 in 152,058 control chromosomes in the GnomAD database, including 19,117 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 0.47 (19117 hom., cov: 32)
• Consequence: ENSG00000302890 ENST00000790297.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.912
• Publications: 30 publications found

Genes affected

ENSG00000302890 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 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
ENSG00000302890	ENST00000790297.1	n.60G>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000302890	ENST00000790298.1	n.30G>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71190 AN: 151940 Hom.: 19080 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.469 AC: 71286 AN: 152058 Hom.: 19117 Cov.: 32 AF XY: 0.466 AC XY: 34599 AN XY: 74326

African (AFR) AF: 0.719 AC: 29845 AN: 41500

American (AMR) AF: 0.404 AC: 6170 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1138 AN: 3468

East Asian (EAS) AF: 0.797 AC: 4102 AN: 5144

South Asian (SAS) AF: 0.534 AC: 2567 AN: 4810

European-Finnish (FIN) AF: 0.285 AC: 3009 AN: 10562

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23184 AN: 67966

Other (OTH) AF: 0.426 AC: 900 AN: 2112

Alfa AF: 0.387 Hom.: 52099

Bravo AF: 0.491

Asia WGS AF: 0.658 AC: 2286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs807624; hg19: chr2-15782471;