12-64990190-C-A

Variant names:

• chr12-64990190-C-A
• rs6581596
• ENST00000649369.1:n.1452C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000649369.1(LINC02389):​n.1452C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: LINC02389 ENST00000649369.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 3 publications found

Genes affected

LINC02389 (HGNC:53316): (long intergenic non-protein coding RNA 2389)

LOC107984522 (HGNC:):

LINC02231 (HGNC:53100): (long intergenic non-protein coding RNA 2231)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984522	XR_001749177.2	n.1115C>A		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02231	NR_146276.1	n.15+2087G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02389	ENST00000649369.1	n.1452C>A		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02389	ENST00000653132.1	n.1424C>A		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02389	ENST00000653464.1	n.1965C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 18243

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.94
DANN	Benign	0.51
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6581596; hg19: chr12-65383970;