6-131956291-C-G

Variant names:

• chr6-131956291-C-G
• rs9402373
• ENST00000435287.2:n.309+5037C>G

Variant summary

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

The ENST00000435287.2(LINC01013):​n.309+5037C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,130 control chromosomes in the GnomAD database, including 2,642 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 0.17 (2642 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 14 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+45336C>G		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+52057C>G		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+32221C>G		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+52057C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000435287.2	n.309+5037C>G		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000440246.2	n.96+6085C>G		intron_variant	Intron 1 of 2	3
LINC01013	ENST00000706294.2	n.183-53566C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25761 AN: 152012 Hom.: 2638 Cov.: 32

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.169 AC: 25784 AN: 152130 Hom.: 2642 Cov.: 32 AF XY: 0.175 AC XY: 12979 AN XY: 74378

African (AFR) AF: 0.0787 AC: 3266 AN: 41506

American (AMR) AF: 0.206 AC: 3147 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3468

East Asian (EAS) AF: 0.405 AC: 2092 AN: 5162

South Asian (SAS) AF: 0.271 AC: 1306 AN: 4822

European-Finnish (FIN) AF: 0.219 AC: 2316 AN: 10564

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12801 AN: 68010

Other (OTH) AF: 0.171 AC: 362 AN: 2114

Alfa AF: 0.0776 Hom.: 90

Bravo AF: 0.166

Asia WGS AF: 0.349 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.0
DANN	Benign	0.74
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs9402373; hg19: chr6-132277431;