chr6-132096424-G-A

Variant names:

• chr6-132096424-G-A
• rs7745875
• ENST00000430428.2:n.204-2507G>A

Variant summary

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

The ENST00000430428.2(LINC01013):​n.204-2507G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0964 in 152,066 control chromosomes in the GnomAD database, including 983 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 0.096 (983 hom., cov: 32)
• Consequence: LINC01013 ENST00000430428.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.372-2507G>A		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.557-2507G>A		intron_variant	Intron 3 of 3
CCN2-AS1	NR_187595.1	n.782-2507G>A		intron_variant	Intron 5 of 5
CCN2-AS1	NR_187596.1	n.489-2507G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000430428.2	n.204-2507G>A		intron_variant	Intron 1 of 1	4
LINC01013	ENST00000440246.2	n.378-2507G>A		intron_variant	Intron 2 of 2	3
LINC01013	ENST00000706295.1	n.155-31104G>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.0964 AC: 14642 AN: 151948 Hom.: 980 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.00598

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.0812

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

GnomAD4 genome AF: 0.0964 AC: 14654 AN: 152066 Hom.: 983 Cov.: 32 AF XY: 0.0932 AC XY: 6925 AN XY: 74340

African (AFR) AF: 0.184 AC: 7626 AN: 41460

American (AMR) AF: 0.0752 AC: 1148 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3468

East Asian (EAS) AF: 0.00599 AC: 31 AN: 5174

South Asian (SAS) AF: 0.0380 AC: 183 AN: 4818

European-Finnish (FIN) AF: 0.0463 AC: 491 AN: 10600

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0705 AC: 4796 AN: 67986

Other (OTH) AF: 0.0803 AC: 169 AN: 2104

Alfa AF: 0.0741 Hom.: 226

Bravo AF: 0.102

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.8
DANN	Benign	0.73
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7745875; hg19: chr6-132417564;