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 ENST00000615716.2(LINC02391):​n.387-38812T>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 ENST00000615716.2 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02391	XR_007063403.1	n.387-22821T>C		intron_variant	Intron 2 of 6
LINC02391	XR_007063404.1	n.387-42449T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02391	ENST00000615716.2	n.387-38812T>C		intron_variant	Intron 2 of 4	5
LINC02391	ENST00000847433.1	n.453-22821T>C		intron_variant	Intron 2 of 5
LINC02391	ENST00000847434.1	n.387-16926T>C		intron_variant	Intron 2 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs337663; hg19: chr12-92705204;