6-131961884-G-A

Variant names:

• chr6-131961884-G-A
• rs2327184
• ENST00000435287.2:n.309+10630G>A

Variant summary

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

The ENST00000435287.2(LINC01013):​n.309+10630G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,138 control chromosomes in the GnomAD database, including 62,393 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 0.91 (62393 hom., cov: 31)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+50929G>A		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.489-47973G>A		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+37814G>A		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+57650G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000435287.2	n.309+10630G>A		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000440246.2	n.96+11678G>A		intron_variant	Intron 1 of 2	3
LINC01013	ENST00000706294.2	n.183-47973G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137642 AN: 152020 Hom.: 62340 Cov.: 31

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.898

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.905 AC: 137752 AN: 152138 Hom.: 62393 Cov.: 31 AF XY: 0.907 AC XY: 67486 AN XY: 74368

African (AFR) AF: 0.900 AC: 37353 AN: 41516

American (AMR) AF: 0.945 AC: 14454 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3071 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5158 AN: 5162

South Asian (SAS) AF: 0.903 AC: 4352 AN: 4818

European-Finnish (FIN) AF: 0.906 AC: 9579 AN: 10576

Middle Eastern (MID) AF: 0.897 AC: 262 AN: 292

European-Non Finnish (NFE) AF: 0.894 AC: 60776 AN: 67990

Other (OTH) AF: 0.919 AC: 1939 AN: 2110

Alfa AF: 0.895 Hom.: 7575

Bravo AF: 0.908

Asia WGS AF: 0.962 AC: 3345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.3
DANN	Benign	0.83
PhyloP100		-0.54

Splicing

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

Publications

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Other links and lift over

dbSNP: rs2327184; hg19: chr6-132283024;