ENST00000435287.2:n.309+4211T>C

Variant names:

• chr6-131955465-T-C
• rs11966728
• ENST00000435287.2:n.309+4211T>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+4211T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,030 control chromosomes in the GnomAD database, including 5,273 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 0.26 (5273 hom., cov: 31)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 4 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 = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+44510T>C		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+51231T>C		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+31395T>C		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+51231T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000435287.2	n.309+4211T>C		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000440246.2	n.96+5259T>C		intron_variant	Intron 1 of 2	3
LINC01013	ENST00000706294.2	n.182+53314T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39615 AN: 151914 Hom.: 5268 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.261 AC: 39641 AN: 152030 Hom.: 5273 Cov.: 31 AF XY: 0.258 AC XY: 19144 AN XY: 74324

African (AFR) AF: 0.291 AC: 12076 AN: 41450

American (AMR) AF: 0.232 AC: 3544 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3468

East Asian (EAS) AF: 0.118 AC: 612 AN: 5170

South Asian (SAS) AF: 0.235 AC: 1131 AN: 4816

European-Finnish (FIN) AF: 0.234 AC: 2471 AN: 10558

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17920 AN: 67972

Other (OTH) AF: 0.275 AC: 581 AN: 2112

Alfa AF: 0.262 Hom.: 916

Bravo AF: 0.262

Asia WGS AF: 0.196 AC: 682 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	5.0
DANN	Benign	0.55
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs11966728; hg19: chr6-132276605;