rs2403456

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-11156267-A-G
• chr11-11156267-A-T

Variant summary

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

The ENST00000525758.1(LINC02752):​n.109-11556A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,030 control chromosomes in the GnomAD database, including 56,033 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 0.85 (56033 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02752	NR_187401.1	n.212-11556A>G		intron_variant	Intron 2 of 2
LINC02752	NR_187402.1	n.224-11556A>G		intron_variant	Intron 3 of 7
LOC105376548	XR_001748126.3	n.141+154T>C		intron_variant	Intron 1 of 2
LOC105376548	XR_007062592.1	n.141+154T>C		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>G		intron_variant	Intron 2 of 6	1
LINC02752	ENST00000647635.1	n.273-12814A>G		intron_variant	Intron 2 of 6
ENSG00000289976	ENST00000702252.2	n.134+154T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129049 AN: 151912 Hom.: 56012 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.849 AC: 129120 AN: 152030 Hom.: 56033 Cov.: 32 AF XY: 0.852 AC XY: 63301 AN XY: 74324

African (AFR) AF: 0.651 AC: 26976 AN: 41448

American (AMR) AF: 0.860 AC: 13147 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3340 AN: 3472

East Asian (EAS) AF: 0.973 AC: 5010 AN: 5150

South Asian (SAS) AF: 0.954 AC: 4600 AN: 4820

European-Finnish (FIN) AF: 0.930 AC: 9867 AN: 10608

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63195 AN: 67938

Other (OTH) AF: 0.881 AC: 1858 AN: 2110

Alfa AF: 0.901 Hom.: 110078

Bravo AF: 0.837

Asia WGS AF: 0.939 AC: 3264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.38
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;