6-131952117-G-C

Variant names:

• chr6-131952117-G-C
• rs6918698
• ENST00000435287.2:n.309+863G>C

Variant summary

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

The ENST00000435287.2(LINC01013):​n.309+863G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,902 control chromosomes in the GnomAD database, including 17,281 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 0.48 (17281 hom., cov: 31)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 46 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435287.2. 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+41162G>C		intron	N/A
	CCN2-AS1	NR_187594.1		n.488+47883G>C		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+28047G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000435287.2	TSL:2	n.309+863G>C		intron	N/A
	LINC01013	ENST00000440246.2	TSL:3	n.96+1911G>C		intron	N/A
	LINC01013	ENST00000706294.2		n.182+49966G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72336 AN: 151786 Hom.: 17252 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.477 AC: 72412 AN: 151902 Hom.: 17281 Cov.: 31 AF XY: 0.474 AC XY: 35155 AN XY: 74232

African (AFR) AF: 0.515 AC: 21323 AN: 41376

American (AMR) AF: 0.455 AC: 6954 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3470

East Asian (EAS) AF: 0.514 AC: 2652 AN: 5158

South Asian (SAS) AF: 0.426 AC: 2052 AN: 4816

European-Finnish (FIN) AF: 0.423 AC: 4460 AN: 10532

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32043 AN: 67962

Other (OTH) AF: 0.470 AC: 993 AN: 2112

Alfa AF: 0.290 Hom.: 606

Bravo AF: 0.485

Asia WGS AF: 0.505 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs6918698; hg19: chr6-132273257;