rs9321315

Variant names:

• chr6-131932136-A-T
• rs9321315
• ENST00000706294.2:n.182+29985A>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+29985A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 151,682 control chromosomes in the GnomAD database, including 911 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 0.10 (911 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+21181A>T		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+27902A>T		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+8066A>T		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+27902A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000706294.2	n.182+29985A>T		intron_variant	Intron 1 of 3
LINC01013	ENST00000706326.1	n.239+29985A>T		intron_variant	Intron 1 of 2
LINC01013	ENST00000706327.1	n.559+27902A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15667 AN: 151564 Hom.: 911 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0998

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.103 AC: 15676 AN: 151682 Hom.: 911 Cov.: 32 AF XY: 0.106 AC XY: 7858 AN XY: 74122

African (AFR) AF: 0.102 AC: 4235 AN: 41318

American (AMR) AF: 0.0768 AC: 1170 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 489 AN: 3464

East Asian (EAS) AF: 0.0951 AC: 490 AN: 5150

South Asian (SAS) AF: 0.199 AC: 958 AN: 4808

European-Finnish (FIN) AF: 0.107 AC: 1128 AN: 10528

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.0998 AC: 6774 AN: 67886

Other (OTH) AF: 0.107 AC: 225 AN: 2098

Alfa AF: 0.105 Hom.: 107

Bravo AF: 0.0982

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.042
DANN	Benign	0.65
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9321315; hg19: chr6-132253276;