chr6-131954052-T-TTAAAATAA

Variant names:

• chr6-131954052-T-TTAAAATAA
• rs3037970
• ENST00000435287.2:n.309+2798_309+2799insTAAAATAA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000435287.2(LINC01013):​n.309+2798_309+2799insTAAAATAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

LINC01013 (HGNC:48987): (long intergenic non-protein coding RNA 1013)

CCN2-AS1 (HGNC:40164): (CCN2 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+43102_371+43103insTAATAAAA		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+49823_488+49824insTAATAAAA		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+29987_327+29988insTAATAAAA		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+49823_488+49824insTAATAAAA		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000435287.2	n.309+2798_309+2799insTAAAATAA		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000706294.1	n.182+51901_182+51902insTAAAATAA		intron_variant	Intron 1 of 3
LINC01013	ENST00000706326.1	n.239+51901_239+51902insTAAAATAA		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3037970; hg19: chr6-132275192;