chr11-11156267-A-T

Variant names:

• chr11-11156267-A-T
• rs2403456
• ENST00000525758.1:n.109-11556A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000525758.1(LINC02752):​n.109-11556A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: LINC02752 ENST00000525758.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 6 publications found

Genes affected

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

ENSG00000289976 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02752	NR_187401.1	n.212-11556A>T		intron_variant	Intron 2 of 2
LINC02752	NR_187402.1	n.224-11556A>T		intron_variant	Intron 3 of 7
LOC105376548	XR_001748126.3	n.141+154T>A		intron_variant	Intron 1 of 2
LOC105376548	XR_007062592.1	n.141+154T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02752	ENST00000525758.1	n.109-11556A>T		intron_variant	Intron 2 of 6	1
LINC02752	ENST00000647635.1	n.273-12814A>T		intron_variant	Intron 2 of 6
ENSG00000289976	ENST00000702252.2	n.134+154T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.42
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs2403456; hg19: chr11-11177814;