ENST00000412306.1:c.223-126958T>A

Variant names:

• chr6-81878548-T-.
• ENST00000418567.2:n.196-32639A>.

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NR_149134.1(LINC02542):​n.147-32639A>. variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 N/A (N/A hom., cov:)
  • Exomes 𝑓: N/A (N/A hom.)
• Consequence: LINC02542 NR_149134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: No publications found

Genes affected

LINC02542 (HGNC:53576): (long intergenic non-protein coding RNA 2542)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_149134.1. 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
	LINC02542	NR_149134.1		n.147-32639A>.		intron	N/A
	LINC02542	NR_149135.1		n.343-32639A>.		intron	N/A
	LINC02542	NR_149136.1		n.98-32639A>.		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02542	ENST00000418567.2	TSL:5	n.196-32639A>.		intron	N/A
	LINC02542	ENST00000660534.3		n.188-32639A>.		intron	N/A
	LINC02542	ENST00000660637.1		n.224-32639A>.		intron	N/A

Frequencies

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

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Splicing

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

Other links and lift over

hg19: chr6-82588265;