rs6917644

Variant names:

• chr6-131944525-A-G
• rs6917644
• ENST00000706294.2:n.182+42374A>G

Variant summary

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

The ENST00000706294.2(LINC01013):​n.182+42374A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,156 control chromosomes in the GnomAD database, including 895 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 0.10 (895 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 7 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 = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+33570A>G		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+40291A>G		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+20455A>G		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+40291A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000706294.2	n.182+42374A>G		intron_variant	Intron 1 of 3
LINC01013	ENST00000706326.1	n.239+42374A>G		intron_variant	Intron 1 of 2
LINC01013	ENST00000706327.1	n.559+40291A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15673 AN: 152038 Hom.: 896 Cov.: 32

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0674

Gnomad SAS AF: 0.0400

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.103 AC: 15682 AN: 152156 Hom.: 895 Cov.: 32 AF XY: 0.0998 AC XY: 7424 AN XY: 74408

African (AFR) AF: 0.0724 AC: 3006 AN: 41520

American (AMR) AF: 0.115 AC: 1757 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3468

East Asian (EAS) AF: 0.0676 AC: 350 AN: 5178

South Asian (SAS) AF: 0.0408 AC: 197 AN: 4826

European-Finnish (FIN) AF: 0.120 AC: 1266 AN: 10590

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8329 AN: 67972

Other (OTH) AF: 0.114 AC: 240 AN: 2114

Alfa AF: 0.111 Hom.: 552

Bravo AF: 0.102

Asia WGS AF: 0.0590 AC: 208 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	9.3
DANN	Benign	0.67
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs6917644; hg19: chr6-132265665;