rs1206736

Variant names:

• chr6-132043095-G-A
• rs1206736
• ENST00000435287.2:n.310-34113G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435287.2(LINC01013):​n.310-34113G>A 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 152,068 control chromosomes in the GnomAD database, including 35,329 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 (35329 hom., cov: 33)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

Genes affected

LINC01013 (HGNC:48987): (long intergenic non-protein coding RNA 1013)

CCN2-AS1 (HGNC:40164): (CCN2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.372-55836G>A		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.556+33171G>A		intron_variant	Intron 3 of 3
CCN2-AS1	NR_187595.1	n.396-31698G>A		intron_variant	Intron 3 of 5
CCN2-AS1	NR_187596.1	n.489-55836G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000435287.2	n.310-34113G>A		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000706294.1	n.251-31698G>A		intron_variant	Intron 2 of 3
LINC01013	ENST00000706295.1	n.154+33171G>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101631 AN: 151950 Hom.: 35287 Cov.: 33

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.629

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: 101731 AN: 152068 Hom.: 35329 Cov.: 33 AF XY: 0.666 AC XY: 49509 AN XY: 74338

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.650

Alfa AF: 0.639 Hom.: 3903

Bravo AF: 0.672

Asia WGS AF: 0.670 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1206736; hg19: chr6-132364235;