rs9384952

Variant names:

• chr6-115638900-T-C
• rs9384952
• ENST00000446525.2:n.113-2636A>G

Variant summary

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

The ENST00000446525.2(LINC02534):​n.113-2636A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,902 control chromosomes in the GnomAD database, including 15,966 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 0.45 (15966 hom., cov: 31)
• Consequence: LINC02534 ENST00000446525.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 2 publications found

Genes affected

LINC02534 (HGNC:53567): (long intergenic non-protein coding RNA 2534)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446525.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02534	NR_134602.1		n.32-2636A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02534	ENST00000446525.2	TSL:3	n.113-2636A>G		intron	N/A
	LINC02534	ENST00000666770.2		n.139-2636A>G		intron	N/A
	LINC02534	ENST00000779568.1		n.128-2636A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68578 AN: 151784 Hom.: 15954 Cov.: 31

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.452 AC: 68635 AN: 151902 Hom.: 15966 Cov.: 31 AF XY: 0.455 AC XY: 33793 AN XY: 74252

African (AFR) AF: 0.564 AC: 23338 AN: 41404

American (AMR) AF: 0.434 AC: 6623 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1669 AN: 3468

East Asian (EAS) AF: 0.418 AC: 2156 AN: 5160

South Asian (SAS) AF: 0.458 AC: 2203 AN: 4808

European-Finnish (FIN) AF: 0.423 AC: 4454 AN: 10534

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26819 AN: 67964

Other (OTH) AF: 0.459 AC: 964 AN: 2102

Alfa AF: 0.412 Hom.: 6664

Bravo AF: 0.452

Asia WGS AF: 0.427 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.0
DANN	Benign	0.65
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs9384952; hg19: chr6-115960064;