rs6940184

Variant names:

• chr6-131936304-G-T
• rs6940184
• ENST00000706294.2:n.182+34153G>T

Variant summary

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

The ENST00000706294.2(LINC01013):​n.182+34153G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,010 control chromosomes in the GnomAD database, including 4,071 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 0.22 (4071 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+25349G>T		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+32070G>T		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+12234G>T		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+32070G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000706294.2	n.182+34153G>T		intron_variant	Intron 1 of 3
LINC01013	ENST00000706326.1	n.239+34153G>T		intron_variant	Intron 1 of 2
LINC01013	ENST00000706327.1	n.559+32070G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33022 AN: 151892 Hom.: 4072 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.217 AC: 33039 AN: 152010 Hom.: 4071 Cov.: 32 AF XY: 0.226 AC XY: 16753 AN XY: 74272

African (AFR) AF: 0.200 AC: 8280 AN: 41458

American (AMR) AF: 0.198 AC: 3029 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1756 AN: 5164

South Asian (SAS) AF: 0.503 AC: 2426 AN: 4820

European-Finnish (FIN) AF: 0.210 AC: 2215 AN: 10542

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13174 AN: 67980

Other (OTH) AF: 0.240 AC: 504 AN: 2104

Alfa AF: 0.210 Hom.: 13286

Bravo AF: 0.211

Asia WGS AF: 0.376 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.51
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs6940184; hg19: chr6-132257444;