ENST00000435287.2:n.309+25747G>A

Variant names:

• chr6-131977001-G-A
• rs928505
• ENST00000435287.2:n.309+25747G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435287.2(LINC01013):​n.309+25747G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,948 control chromosomes in the GnomAD database, including 14,722 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 0.42 (14722 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 5 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+66046G>A		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.489-32856G>A		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.328-32856G>A		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+72767G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000435287.2	n.309+25747G>A		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000440246.2	n.96+26795G>A		intron_variant	Intron 1 of 2	3
LINC01013	ENST00000706294.2	n.183-32856G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64466 AN: 151830 Hom.: 14703 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.425 AC: 64517 AN: 151948 Hom.: 14722 Cov.: 32 AF XY: 0.434 AC XY: 32234 AN XY: 74260

African (AFR) AF: 0.259 AC: 10749 AN: 41442

American (AMR) AF: 0.548 AC: 8359 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1313 AN: 3466

East Asian (EAS) AF: 0.757 AC: 3912 AN: 5168

South Asian (SAS) AF: 0.492 AC: 2368 AN: 4812

European-Finnish (FIN) AF: 0.535 AC: 5641 AN: 10536

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.452 AC: 30742 AN: 67948

Other (OTH) AF: 0.455 AC: 959 AN: 2108

Alfa AF: 0.443 Hom.: 66096

Bravo AF: 0.420

Asia WGS AF: 0.659 AC: 2291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.74
DANN	Benign	0.74
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs928505; hg19: chr6-132298141;