rs952361

Variant names:

• chr11-11164418-G-A
• rs952361
• ENST00000525758.1:n.109-3405G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-11164418-G-A
• chr11-11164418-G-C
• chr11-11164418-G-T

Variant summary

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

The ENST00000525758.1(LINC02752):​n.109-3405G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,556 control chromosomes in the GnomAD database, including 17,882 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 0.48 (17882 hom., cov: 30)
• Consequence: LINC02752 ENST00000525758.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02752	NR_187401.1	n.212-3405G>A		intron_variant	Intron 2 of 2
LINC02752	NR_187402.1	n.224-3405G>A		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02752	ENST00000525758.1	n.109-3405G>A		intron_variant	Intron 2 of 6	1
LINC02752	ENST00000647635.1	n.273-4663G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72593 AN: 151440 Hom.: 17840 Cov.: 30

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.480 AC: 72699 AN: 151556 Hom.: 17882 Cov.: 30 AF XY: 0.478 AC XY: 35365 AN XY: 74016

African (AFR) AF: 0.597 AC: 24656 AN: 41308

American (AMR) AF: 0.418 AC: 6368 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1397 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1917 AN: 5086

South Asian (SAS) AF: 0.432 AC: 2070 AN: 4792

European-Finnish (FIN) AF: 0.471 AC: 4927 AN: 10452

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29972 AN: 67904

Other (OTH) AF: 0.456 AC: 961 AN: 2108

Alfa AF: 0.440 Hom.: 8063

Bravo AF: 0.485

Asia WGS AF: 0.468 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.1
DANN	Benign	0.61
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs952361; hg19: chr11-11185965;