rs2095252

Variant names:

• chr6-131962448-C-T
• rs2095252
• ENST00000435287.2:n.309+11194C>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+11194C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,094 control chromosomes in the GnomAD database, including 9,274 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 0.31 (9274 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+51493C>T		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.489-47409C>T		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+38378C>T		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+58214C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000435287.2	n.309+11194C>T		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000440246.2	n.96+12242C>T		intron_variant	Intron 1 of 2	3
LINC01013	ENST00000706294.2	n.183-47409C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47915 AN: 151976 Hom.: 9275 Cov.: 32

Gnomad AFR AF: 0.0860

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.315 AC: 47907 AN: 152094 Hom.: 9274 Cov.: 32 AF XY: 0.313 AC XY: 23298 AN XY: 74338

African (AFR) AF: 0.0858 AC: 3566 AN: 41540

American (AMR) AF: 0.300 AC: 4576 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1088 AN: 5170

South Asian (SAS) AF: 0.408 AC: 1969 AN: 4826

European-Finnish (FIN) AF: 0.372 AC: 3925 AN: 10552

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29790 AN: 67956

Other (OTH) AF: 0.337 AC: 712 AN: 2114

Alfa AF: 0.413 Hom.: 4525

Bravo AF: 0.297

Asia WGS AF: 0.258 AC: 897 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	1.9
DANN	Benign	0.81
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs2095252; hg19: chr6-132283588;