chr12-92290575-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02391	XR_007063403.1	n.387-1968G>A		intron_variant	Intron 2 of 6
LINC02391	XR_007063404.1	n.387-21596G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02391	ENST00000615716.2	n.387-17959G>A		intron_variant	Intron 2 of 4	5
LINC02391	ENST00000847433.1	n.453-1968G>A		intron_variant	Intron 2 of 5
LINC02391	ENST00000847434.1	n.464+3850G>A		intron_variant	Intron 3 of 5

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 v4.3

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;