rs2151532

Variant names:

• chr6-131953590-G-A
• rs2151532
• ENST00000435287.2:n.309+2336G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-131953590-G-A
• chr6-131953590-G-C
• chr6-131953590-G-T

Variant summary

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

The ENST00000435287.2(LINC01013):​n.309+2336G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,188 control chromosomes in the GnomAD database, including 58,540 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 (58540 hom., cov: 31)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 8 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 (NFE) allele frequency at 95% confidence interval = 0.894 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+42635G>A		intron	N/A
	CCN2-AS1	NR_187594.1		n.488+49356G>A		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+29520G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000435287.2	TSL:2	n.309+2336G>A		intron	N/A
	LINC01013	ENST00000440246.2	TSL:3	n.96+3384G>A		intron	N/A
	LINC01013	ENST00000706294.2		n.182+51439G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133181 AN: 152070 Hom.: 58493 Cov.: 31

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.876 AC: 133286 AN: 152188 Hom.: 58540 Cov.: 31 AF XY: 0.872 AC XY: 64874 AN XY: 74384

African (AFR) AF: 0.882 AC: 36618 AN: 41528

American (AMR) AF: 0.784 AC: 11982 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3007 AN: 3472

East Asian (EAS) AF: 0.732 AC: 3781 AN: 5162

South Asian (SAS) AF: 0.882 AC: 4247 AN: 4814

European-Finnish (FIN) AF: 0.898 AC: 9504 AN: 10588

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61206 AN: 68020

Other (OTH) AF: 0.878 AC: 1852 AN: 2110

Alfa AF: 0.888 Hom.: 77422

Bravo AF: 0.867

Asia WGS AF: 0.826 AC: 2873 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	11
DANN	Benign	0.70
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2151532; hg19: chr6-132274730;