rs337663

Variant names:

• chr12-92311428-A-G
• rs337663
• ENST00000615716.2:n.387-38812T>C

Variant summary

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

The ENST00000847433.1(LINC02391):​n.453-22821T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,128 control chromosomes in the GnomAD database, including 26,318 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 0.58 (26318 hom., cov: 32)
• Consequence: LINC02391 ENST00000847433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 8 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847433.1. 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
	LINC02391	ENST00000615716.2	TSL:5	n.387-38812T>C		intron	N/A
	LINC02391	ENST00000847433.1		n.453-22821T>C		intron	N/A
	LINC02391	ENST00000847434.1		n.387-16926T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87922 AN: 152010 Hom.: 26296 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.578 AC: 87995 AN: 152128 Hom.: 26318 Cov.: 32 AF XY: 0.573 AC XY: 42621 AN XY: 74384

African (AFR) AF: 0.736 AC: 30547 AN: 41518

American (AMR) AF: 0.459 AC: 7008 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2024 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3274 AN: 5174

South Asian (SAS) AF: 0.457 AC: 2206 AN: 4822

European-Finnish (FIN) AF: 0.511 AC: 5401 AN: 10574

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.526 AC: 35747 AN: 67976

Other (OTH) AF: 0.569 AC: 1200 AN: 2110

Alfa AF: 0.535 Hom.: 12284

Bravo AF: 0.582

Asia WGS AF: 0.564 AC: 1963 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.49
DANN	Benign	0.64
PhyloP100		-1.1

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: rs337663;

hg19: chr12-92705204;