6-132042367-A-G

Variant names:

• chr6-132042367-A-G
• rs975515
• ENST00000435287.2:n.310-34841A>G

Variant summary

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

The ENST00000435287.2(LINC01013):​n.310-34841A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,028 control chromosomes in the GnomAD database, including 35,316 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 0.67 (35316 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCN2-AS1	NR_187593.1		n.372-56564A>G		intron	N/A
	CCN2-AS1	NR_187594.1		n.556+32443A>G		intron	N/A
	CCN2-AS1	NR_187595.1		n.396-32426A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000435287.2	TSL:2	n.310-34841A>G		intron	N/A
	LINC01013	ENST00000440246.2	TSL:3	n.97-48079A>G		intron	N/A
	LINC01013	ENST00000706294.2		n.251-32426A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101597 AN: 151910 Hom.: 35274 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.669 AC: 101697 AN: 152028 Hom.: 35316 Cov.: 32 AF XY: 0.666 AC XY: 49483 AN XY: 74298

African (AFR) AF: 0.868 AC: 36012 AN: 41494

American (AMR) AF: 0.535 AC: 8155 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1900 AN: 3468

East Asian (EAS) AF: 0.627 AC: 3241 AN: 5166

South Asian (SAS) AF: 0.614 AC: 2955 AN: 4816

European-Finnish (FIN) AF: 0.650 AC: 6864 AN: 10556

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40478 AN: 67970

Other (OTH) AF: 0.650 AC: 1372 AN: 2110

Alfa AF: 0.606 Hom.: 39650

Bravo AF: 0.672

Asia WGS AF: 0.666 AC: 2318 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	0.63
DANN	Benign	0.32
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs975515; hg19: chr6-132363507;