6-131960658-A-G

Variant names:

• chr6-131960658-A-G
• rs9483364
• ENST00000435287.2:n.309+9404A>G

Variant summary

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

The ENST00000435287.2(LINC01013):​n.309+9404A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,026 control chromosomes in the GnomAD database, including 33,587 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 0.66 (33587 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435287.2. 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+49703A>G		intron	N/A
	CCN2-AS1	NR_187594.1		n.489-49199A>G		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+36588A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000435287.2	TSL:2	n.309+9404A>G		intron	N/A
	LINC01013	ENST00000440246.2	TSL:3	n.96+10452A>G		intron	N/A
	LINC01013	ENST00000706294.2		n.183-49199A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100652 AN: 151908 Hom.: 33564 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.663 AC: 100725 AN: 152026 Hom.: 33587 Cov.: 32 AF XY: 0.659 AC XY: 49002 AN XY: 74318

African (AFR) AF: 0.592 AC: 24539 AN: 41426

American (AMR) AF: 0.613 AC: 9371 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2133 AN: 3460

East Asian (EAS) AF: 0.660 AC: 3416 AN: 5176

South Asian (SAS) AF: 0.671 AC: 3236 AN: 4822

European-Finnish (FIN) AF: 0.672 AC: 7098 AN: 10556

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48679 AN: 67992

Other (OTH) AF: 0.640 AC: 1348 AN: 2106

Alfa AF: 0.693 Hom.: 78957

Bravo AF: 0.655

Asia WGS AF: 0.678 AC: 2354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.35
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9483364; hg19: chr6-132281798;