ENST00000435287.2:n.309+2798_309+2799insTAAAA

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000435287.2(LINC01013):​n.309+2798_309+2799insTAAAA 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: 𝑓 0.54 (22555 hom., cov: 0)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 2 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435287.2. 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
	CCN2-AS1	NR_187593.1		n.371+43098_371+43102dupTAAAA		intron	N/A
	CCN2-AS1	NR_187594.1		n.488+49819_488+49823dupTAAAA		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+29983_327+29987dupTAAAA		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000435287.2	TSL:2	n.309+2798_309+2799insTAAAA		intron	N/A
	LINC01013	ENST00000440246.2	TSL:3	n.96+3846_96+3847insTAAAA		intron	N/A
	LINC01013	ENST00000706294.2		n.182+51901_182+51902insTAAAA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81270 AN: 151176 Hom.: 22512 Cov.: 0

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.538 AC: 81367 AN: 151296 Hom.: 22555 Cov.: 0 AF XY: 0.535 AC XY: 39540 AN XY: 73896

African (AFR) AF: 0.695 AC: 28626 AN: 41162

American (AMR) AF: 0.485 AC: 7382 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1370 AN: 3456

East Asian (EAS) AF: 0.522 AC: 2676 AN: 5126

South Asian (SAS) AF: 0.498 AC: 2393 AN: 4808

European-Finnish (FIN) AF: 0.463 AC: 4820 AN: 10402

Middle Eastern (MID) AF: 0.563 AC: 162 AN: 288

European-Non Finnish (NFE) AF: 0.477 AC: 32310 AN: 67802

Other (OTH) AF: 0.529 AC: 1116 AN: 2108

Alfa AF: 0.495 Hom.: 2028

Asia WGS AF: 0.560 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.028

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: rs3037970; hg19: chr6-132275192;