6-131955880-G-A

Variant names:

• chr6-131955880-G-A
• rs12198610
• ENST00000435287.2:n.309+4626G>A

Variant summary

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

The ENST00000435287.2(LINC01013):​n.309+4626G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,080 control chromosomes in the GnomAD database, including 6,806 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 0.29 (6806 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.653
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+44925G>A		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+51646G>A		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+31810G>A		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+51646G>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+4626G>A		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000440246.2	n.96+5674G>A		intron_variant	Intron 1 of 2	3
LINC01013	ENST00000706294.2	n.182+53729G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44266 AN: 151962 Hom.: 6794 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.291 AC: 44317 AN: 152080 Hom.: 6806 Cov.: 32 AF XY: 0.287 AC XY: 21353 AN XY: 74338

African (AFR) AF: 0.396 AC: 16444 AN: 41478

American (AMR) AF: 0.243 AC: 3713 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3468

East Asian (EAS) AF: 0.119 AC: 615 AN: 5164

South Asian (SAS) AF: 0.235 AC: 1135 AN: 4824

European-Finnish (FIN) AF: 0.235 AC: 2483 AN: 10574

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17959 AN: 67972

Other (OTH) AF: 0.300 AC: 633 AN: 2110

Alfa AF: 0.278 Hom.: 1305

Bravo AF: 0.296

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.25
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs12198610; hg19: chr6-132277020;