6-131944324-C-T

Variant names:

• chr6-131944324-C-T
• rs1931003
• ENST00000706294.2:n.182+42173C>T

Variant summary

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

The NR_187593.1(CCN2-AS1):​n.371+33369C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,842 control chromosomes in the GnomAD database, including 13,663 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 (13663 hom., cov: 31)
• Consequence: CCN2-AS1 NR_187593.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187593.1. 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+33369C>T		intron	N/A
	CCN2-AS1	NR_187594.1		n.488+40090C>T		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+20254C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000706294.2		n.182+42173C>T		intron	N/A
	LINC01013	ENST00000706326.1		n.239+42173C>T		intron	N/A
	LINC01013	ENST00000706327.1		n.559+40090C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64373 AN: 151722 Hom.: 13650 Cov.: 31

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.424 AC: 64424 AN: 151842 Hom.: 13663 Cov.: 31 AF XY: 0.421 AC XY: 31227 AN XY: 74210

African (AFR) AF: 0.388 AC: 16059 AN: 41396

American (AMR) AF: 0.426 AC: 6495 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1208 AN: 3466

East Asian (EAS) AF: 0.536 AC: 2762 AN: 5152

South Asian (SAS) AF: 0.389 AC: 1868 AN: 4802

European-Finnish (FIN) AF: 0.379 AC: 3991 AN: 10542

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30533 AN: 67918

Other (OTH) AF: 0.418 AC: 879 AN: 2102

Alfa AF: 0.439 Hom.: 22478

Bravo AF: 0.430

Asia WGS AF: 0.494 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.25
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1931003; hg19: chr6-132265464;