rs9604529

Positions:

• chr13-113919624-A-G
• chr13-113919624-A-T

Variant summary

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

The NR_164112.1(LINC00452):​n.1111A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,289,082 control chromosomes in the GnomAD database, including 26,097 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 0.24 (5131 hom., cov: 33)
  • Exomes 𝑓: 0.19 (20966 hom.)
• Consequence: LINC00452 NR_164112.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

Genes affected

LINC00452 (HGNC:42800): (long intergenic non-protein coding RNA 452)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00452	NR_164112.1	n.1111A>G		non_coding_transcript_exon_variant	6/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00452	ENST00000609661.5	n.801A>G		non_coding_transcript_exon_variant	5/8	5
LINC00452	ENST00000426859.1	n.1111A>G		non_coding_transcript_exon_variant	6/8	2
LINC00452	ENST00000671032.1	n.433A>G		non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35755 AN: 151952 Hom.: 5104 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.0495

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.234

GnomAD3 exomes AF: 0.166 AC: 22294 AN: 134502 Hom.: 2274 AF XY: 0.162 AC XY: 11875 AN XY: 73238

Gnomad AFR exome AF: 0.404

Gnomad AMR exome AF: 0.141

Gnomad ASJ exome AF: 0.228

Gnomad EAS exome AF: 0.0514

Gnomad SAS exome AF: 0.102

Gnomad FIN exome AF: 0.106

Gnomad NFE exome AF: 0.193

Gnomad OTH exome AF: 0.181

GnomAD4 exome AF: 0.186 AC: 211075 AN: 1137012 Hom.: 20966 Cov.: 32 AF XY: 0.182 AC XY: 101605 AN XY: 557718

Gnomad4 AFR exome AF: 0.407

Gnomad4 AMR exome AF: 0.143

Gnomad4 ASJ exome AF: 0.230

Gnomad4 EAS exome AF: 0.0512

Gnomad4 SAS exome AF: 0.102

Gnomad4 FIN exome AF: 0.117

Gnomad4 NFE exome AF: 0.190

Gnomad4 OTH exome AF: 0.192

GnomAD4 genome AF: 0.236 AC: 35839 AN: 152070 Hom.: 5131 Cov.: 33 AF XY: 0.228 AC XY: 16920 AN XY: 74358

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.0494

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.232

Alfa AF: 0.195 Hom.: 5295

Bravo AF: 0.253

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9604529; hg19: chr13-114622597;