ENST00000615716.2:n.387-17959G>A

Variant names:

• chr12-92290575-C-T
• rs337656
• ENST00000615716.2:n.387-17959G>A

Variant summary

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

The ENST00000615716.2(LINC02391):​n.387-17959G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,162 control chromosomes in the GnomAD database, including 47,974 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 0.79 (47974 hom., cov: 31)
• Consequence: LINC02391 ENST00000615716.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 7 publications found

Genes affected

LINC02391 (HGNC:53318): (long intergenic non-protein coding RNA 2391)

ENSG00000310158 (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 = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615716.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02391	ENST00000615716.2	TSL:5	n.387-17959G>A		intron	N/A
	LINC02391	ENST00000847433.1		n.453-1968G>A		intron	N/A
	LINC02391	ENST00000847434.1		n.464+3850G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120508 AN: 152044 Hom.: 47945 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.793 AC: 120594 AN: 152162 Hom.: 47974 Cov.: 31 AF XY: 0.797 AC XY: 59279 AN XY: 74380

African (AFR) AF: 0.771 AC: 31984 AN: 41488

American (AMR) AF: 0.841 AC: 12858 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2756 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5167 AN: 5184

South Asian (SAS) AF: 0.880 AC: 4241 AN: 4822

European-Finnish (FIN) AF: 0.774 AC: 8186 AN: 10582

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52754 AN: 67996

Other (OTH) AF: 0.797 AC: 1685 AN: 2114

Alfa AF: 0.785 Hom.: 90028

Bravo AF: 0.797

Asia WGS AF: 0.928 AC: 3229 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	1.2
DANN	Benign	0.40
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs337656; hg19: chr12-92684351;