6-131936884-T-C

Variant names:

• chr6-131936884-T-C
• rs12523697
• ENST00000706294.2:n.182+34733T>C

Variant summary

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

The ENST00000706294.2(LINC01013):​n.182+34733T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,180 control chromosomes in the GnomAD database, including 3,787 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 0.21 (3787 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000706294.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCN2-AS1	NR_187593.1		n.371+25929T>C		intron	N/A
	CCN2-AS1	NR_187594.1		n.488+32650T>C		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+12814T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000706294.2		n.182+34733T>C		intron	N/A
	LINC01013	ENST00000706326.1		n.239+34733T>C		intron	N/A
	LINC01013	ENST00000706327.1		n.559+32650T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31370 AN: 152062 Hom.: 3793 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.206 AC: 31375 AN: 152180 Hom.: 3787 Cov.: 32 AF XY: 0.213 AC XY: 15861 AN XY: 74390

African (AFR) AF: 0.158 AC: 6553 AN: 41518

American (AMR) AF: 0.193 AC: 2956 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1382 AN: 3470

East Asian (EAS) AF: 0.348 AC: 1795 AN: 5162

South Asian (SAS) AF: 0.506 AC: 2442 AN: 4828

European-Finnish (FIN) AF: 0.209 AC: 2211 AN: 10584

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13260 AN: 68004

Other (OTH) AF: 0.226 AC: 478 AN: 2112

Alfa AF: 0.216 Hom.: 1624

Bravo AF: 0.198

Asia WGS AF: 0.375 AC: 1304 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs12523697; hg19: chr6-132258024;