6-131957342-T-C

Variant names:

• chr6-131957342-T-C
• rs1931002
• ENST00000435287.2:n.309+6088T>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+6088T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 152,244 control chromosomes in the GnomAD database, including 58,852 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 0.88 (58852 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 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+46387T>C		intron	N/A
	CCN2-AS1	NR_187594.1		n.489-52515T>C		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+33272T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000435287.2	TSL:2	n.309+6088T>C		intron	N/A
	LINC01013	ENST00000440246.2	TSL:3	n.96+7136T>C		intron	N/A
	LINC01013	ENST00000706294.2		n.183-52515T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133554 AN: 152126 Hom.: 58805 Cov.: 32

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.878 AC: 133659 AN: 152244 Hom.: 58852 Cov.: 32 AF XY: 0.874 AC XY: 65076 AN XY: 74424

African (AFR) AF: 0.881 AC: 36597 AN: 41550

American (AMR) AF: 0.790 AC: 12078 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3013 AN: 3472

East Asian (EAS) AF: 0.731 AC: 3783 AN: 5174

South Asian (SAS) AF: 0.884 AC: 4258 AN: 4818

European-Finnish (FIN) AF: 0.898 AC: 9522 AN: 10602

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61452 AN: 68012

Other (OTH) AF: 0.882 AC: 1865 AN: 2114

Alfa AF: 0.891 Hom.: 41602

Bravo AF: 0.870

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.58
DANN	Benign	0.65
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1931002;

hg19: chr6-132278482;