rs6910279

Variant names:

• chr6-131932924-G-A
• rs6910279
• ENST00000706294.2:n.182+30773G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-131932924-G-A
• chr6-131932924-G-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+30773G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,108 control chromosomes in the GnomAD database, including 47,805 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 0.79 (47805 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000706294.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCN2-AS1	NR_187593.1		n.371+21969G>A		intron	N/A
	CCN2-AS1	NR_187594.1		n.488+28690G>A		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+8854G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000706294.2		n.182+30773G>A		intron	N/A
	LINC01013	ENST00000706326.1		n.239+30773G>A		intron	N/A
	LINC01013	ENST00000706327.1		n.559+28690G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120299 AN: 151990 Hom.: 47757 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.792 AC: 120398 AN: 152108 Hom.: 47805 Cov.: 32 AF XY: 0.793 AC XY: 58965 AN XY: 74354

African (AFR) AF: 0.794 AC: 32929 AN: 41464

American (AMR) AF: 0.765 AC: 11697 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2950 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3179 AN: 5174

South Asian (SAS) AF: 0.766 AC: 3697 AN: 4824

European-Finnish (FIN) AF: 0.850 AC: 8981 AN: 10572

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54268 AN: 68004

Other (OTH) AF: 0.803 AC: 1696 AN: 2112

Alfa AF: 0.792 Hom.: 128635

Bravo AF: 0.783

Asia WGS AF: 0.660 AC: 2297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.21
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs6910279; hg19: chr6-132254064;