rs9384952

Positions:

• chr6-115638900-T-C

Variant summary

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

The NR_134602.1(LINC02534):​n.32-2636A>G variant causes a intron, non coding transcript 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 NR_134602.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02534	NR_134602.1	n.32-2636A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02534	ENST00000446525.2	n.113-2636A>G		intron_variant, non_coding_transcript_variant		3
LINC02534	ENST00000666770.1	n.113-2636A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.459

Alfa AF: 0.412 Hom.: 5926

Bravo AF: 0.452

Asia WGS AF: 0.427 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9384952; hg19: chr6-115960064;