rs7747601

Variant names:

• chr6-131955764-A-G
• rs7747601
• ENST00000435287.2:n.309+4510A>G

Variant summary

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

The ENST00000435287.2(LINC01013):​n.309+4510A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,214 control chromosomes in the GnomAD database, including 2,336 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 0.15 (2336 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+44809A>G		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+51530A>G		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+31694A>G		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+51530A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000435287.2	n.309+4510A>G		intron_variant	Intron 1 of 1	2
LINC01013	ENST00000440246.2	n.96+5558A>G		intron_variant	Intron 1 of 2	3
LINC01013	ENST00000706294.2	n.182+53613A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23024 AN: 152096 Hom.: 2334 Cov.: 32

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.0972

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.151 AC: 23031 AN: 152214 Hom.: 2336 Cov.: 32 AF XY: 0.157 AC XY: 11663 AN XY: 74422

African (AFR) AF: 0.0369 AC: 1532 AN: 41560

American (AMR) AF: 0.197 AC: 3006 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0972 AC: 337 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2063 AN: 5156

South Asian (SAS) AF: 0.266 AC: 1284 AN: 4826

European-Finnish (FIN) AF: 0.215 AC: 2277 AN: 10590

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.178 AC: 12086 AN: 68006

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.167 Hom.: 878

Bravo AF: 0.147

Asia WGS AF: 0.340 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.82
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs7747601; hg19: chr6-132276904; COSMIC: COSV63466587;