rs12527379

Variant names:

• chr6-131958700-G-A
• rs12527379
• ENST00000435287.2:n.309+7446G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-131958700-G-A
• chr6-131958700-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+7446G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,102 control chromosomes in the GnomAD database, including 9,328 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 0.32 (9328 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 6 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+47745G>A		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.489-51157G>A		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+34630G>A		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+54466G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000435287.2	n.309+7446G>A		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000440246.2	n.96+8494G>A		intron_variant	Intron 1 of 2	3
LINC01013	ENST00000706294.2	n.183-51157G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48167 AN: 151984 Hom.: 9329 Cov.: 32

Gnomad AFR AF: 0.0865

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.317 AC: 48163 AN: 152102 Hom.: 9328 Cov.: 32 AF XY: 0.315 AC XY: 23451 AN XY: 74334

African (AFR) AF: 0.0863 AC: 3583 AN: 41512

American (AMR) AF: 0.322 AC: 4925 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1218 AN: 5174

South Asian (SAS) AF: 0.404 AC: 1945 AN: 4820

European-Finnish (FIN) AF: 0.371 AC: 3921 AN: 10562

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29579 AN: 67972

Other (OTH) AF: 0.336 AC: 708 AN: 2110

Alfa AF: 0.363 Hom.: 4395

Bravo AF: 0.302

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.60
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs12527379; hg19: chr6-132279840;