13-113919624-A-G

Variant names:

• chr13-113919624-A-G
• rs9604529
• ENST00000426859.1:n.1111A>G

Variant summary

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

The ENST00000426859.1(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 ENST00000426859.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 21 publications found

Genes affected

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

ENSG00000293677 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426859.1. 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
	LINC00452	NR_164112.1		n.1111A>G		non_coding_transcript_exon	Exon 6 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00452	ENST00000426859.1	TSL:2	n.1111A>G		non_coding_transcript_exon	Exon 6 of 8
	LINC00452	ENST00000671032.1		n.433A>G		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000293677	ENST00000717691.1		n.688A>G		non_coding_transcript_exon	Exon 4 of 7

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

GnomAD2 exomes AF: 0.166 AC: 22294 AN: 134502 AF XY: 0.162

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 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

African (AFR) AF: 0.407 AC: 9934 AN: 24394

American (AMR) AF: 0.143 AC: 4030 AN: 28252

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 3672 AN: 15936

East Asian (EAS) AF: 0.0512 AC: 656 AN: 12820

South Asian (SAS) AF: 0.102 AC: 7791 AN: 76196

European-Finnish (FIN) AF: 0.117 AC: 1530 AN: 13080

Middle Eastern (MID) AF: 0.180 AC: 790 AN: 4394

European-Non Finnish (NFE) AF: 0.190 AC: 174721 AN: 920426

Other (OTH) AF: 0.192 AC: 7951 AN: 41514

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

African (AFR) AF: 0.397 AC: 16456 AN: 41484

American (AMR) AF: 0.189 AC: 2890 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 823 AN: 3464

East Asian (EAS) AF: 0.0494 AC: 255 AN: 5162

South Asian (SAS) AF: 0.102 AC: 493 AN: 4828

European-Finnish (FIN) AF: 0.102 AC: 1082 AN: 10582

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12919 AN: 67950

Other (OTH) AF: 0.232 AC: 489 AN: 2110

Alfa AF: 0.209 Hom.: 11097

Bravo AF: 0.253

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.34
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs9604529; hg19: chr13-114622597;