ENST00000435287.2:n.309+9470C>T

Variant names:

• chr6-131960724-C-T
• rs10872386
• ENST00000435287.2:n.309+9470C>T

Variant summary

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

The ENST00000435287.2(LINC01013):​n.309+9470C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,964 control chromosomes in the GnomAD database, including 2,551 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 0.16 (2551 hom., cov: 31)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+49769C>T		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.489-49133C>T		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+36654C>T		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+56490C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000435287.2	n.309+9470C>T		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000440246.2	n.96+10518C>T		intron_variant	Intron 1 of 2	3
LINC01013	ENST00000706294.2	n.183-49133C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24761 AN: 151846 Hom.: 2550 Cov.: 31

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.163 AC: 24776 AN: 151964 Hom.: 2551 Cov.: 31 AF XY: 0.166 AC XY: 12359 AN XY: 74260

African (AFR) AF: 0.0492 AC: 2037 AN: 41436

American (AMR) AF: 0.191 AC: 2923 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0878 AC: 304 AN: 3464

East Asian (EAS) AF: 0.413 AC: 2135 AN: 5172

South Asian (SAS) AF: 0.221 AC: 1063 AN: 4812

European-Finnish (FIN) AF: 0.235 AC: 2473 AN: 10534

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13350 AN: 67950

Other (OTH) AF: 0.167 AC: 352 AN: 2106

Alfa AF: 0.168 Hom.: 274

Bravo AF: 0.157

Asia WGS AF: 0.339 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.0
DANN	Benign	0.63
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs10872386; hg19: chr6-132281864;