ENST00000525758.1:n.108+10238T>G

Variant names:

• chr11-11130773-T-G
• rs1394119
• ENST00000525758.1:n.108+10238T>G

Variant summary

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

The ENST00000525758.1(LINC02752):​n.108+10238T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,980 control chromosomes in the GnomAD database, including 12,305 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 0.38 (12305 hom., cov: 32)
• Consequence: LINC02752 ENST00000525758.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 2 publications found

Genes affected

LINC02752 (HGNC:54272): (long intergenic non-protein coding RNA 2752)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02752	NR_187401.1	n.211+12824T>G		intron_variant	Intron 2 of 2
LINC02752	NR_187402.1	n.223+10238T>G		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02752	ENST00000525758.1	n.108+10238T>G		intron_variant	Intron 2 of 6	1
LINC02752	ENST00000647635.1	n.272+12824T>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58357 AN: 151860 Hom.: 12306 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.384 AC: 58373 AN: 151980 Hom.: 12305 Cov.: 32 AF XY: 0.383 AC XY: 28424 AN XY: 74278

African (AFR) AF: 0.209 AC: 8689 AN: 41504

American (AMR) AF: 0.467 AC: 7134 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1268 AN: 5168

South Asian (SAS) AF: 0.336 AC: 1616 AN: 4814

European-Finnish (FIN) AF: 0.404 AC: 4271 AN: 10560

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32295 AN: 67882

Other (OTH) AF: 0.409 AC: 862 AN: 2108

Alfa AF: 0.405 Hom.: 2048

Bravo AF: 0.381

Asia WGS AF: 0.277 AC: 961 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.56
DANN	Benign	0.73
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1394119; hg19: chr11-11152320;