rs4910266

Variant names:

• chr11-11175086-T-A
• rs4910266
• ENST00000525758.1:n.562-4821T>A

Your query was ambiguous. Multiple possible variants found:

• chr11-11175086-T-A
• chr11-11175086-T-C

Variant summary

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

The ENST00000525758.1(LINC02752):​n.562-4821T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,152 control chromosomes in the GnomAD database, including 6,047 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 0.27 (6047 hom., cov: 33)
• Consequence: LINC02752 ENST00000525758.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.972
• 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=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525758.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02752	NR_187402.1		n.677-4821T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02752	ENST00000525758.1	TSL:1	n.562-4821T>A		intron	N/A
	LINC02752	ENST00000647635.1		n.391-4821T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41398 AN: 152034 Hom.: 6048 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.272 AC: 41416 AN: 152152 Hom.: 6047 Cov.: 33 AF XY: 0.269 AC XY: 20045 AN XY: 74412

African (AFR) AF: 0.191 AC: 7952 AN: 41526

American (AMR) AF: 0.268 AC: 4098 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1300 AN: 3472

East Asian (EAS) AF: 0.173 AC: 893 AN: 5174

South Asian (SAS) AF: 0.309 AC: 1489 AN: 4822

European-Finnish (FIN) AF: 0.218 AC: 2306 AN: 10584

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22249 AN: 67966

Other (OTH) AF: 0.324 AC: 684 AN: 2110

Alfa AF: 0.284 Hom.: 794

Bravo AF: 0.275

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	17
DANN	Benign	0.92
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs4910266; hg19: chr11-11196633;