6-131996124-C-T

Variant names:

• chr6-131996124-C-T
• rs957535
• ENST00000435287.2:n.309+44870C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435287.2(LINC01013):​n.309+44870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0847 in 152,148 control chromosomes in the GnomAD database, including 1,576 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 0.085 (1576 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+85169C>T		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.489-13733C>T		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.328-13733C>T		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+91890C>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+44870C>T		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000706294.1	n.183-13733C>T		intron_variant	Intron 1 of 3
LINC01013	ENST00000706295.1	n.87-13733C>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12860 AN: 152030 Hom.: 1570 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.00358

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0724

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

GnomAD4 genome AF: 0.0847 AC: 12892 AN: 152148 Hom.: 1576 Cov.: 32 AF XY: 0.0824 AC XY: 6130 AN XY: 74386

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.0378

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0323

Gnomad4 FIN AF: 0.00358

Gnomad4 NFE AF: 0.0111

Gnomad4 OTH AF: 0.0716

Alfa AF: 0.0250 Hom.: 121

Bravo AF: 0.0935

Asia WGS AF: 0.0230 AC: 82 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	6.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs957535; hg19: chr6-132317264;