11-45426540-T-G

Variant names:

• chr11-45426540-T-G
• rs2046733
• ENST00000528445.1:n.536-39255A>C

Variant summary

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

The ENST00000781084.1(LINC02687):​n.75-35376T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,026 control chromosomes in the GnomAD database, including 5,761 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 0.26 (5761 hom., cov: 31)
• Consequence: LINC02687 ENST00000781084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 5 publications found

Genes affected

ENSG00000255041 (HGNC:):

LINC02687 (HGNC:54187): (long intergenic non-protein coding RNA 2687)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000781084.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255041	ENST00000528445.1	TSL:5	n.536-39255A>C		intron	N/A
	LINC02687	ENST00000781084.1		n.75-35376T>G		intron	N/A
	LINC02687	ENST00000781085.1		n.110-16197T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40191 AN: 151908 Hom.: 5752 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.265 AC: 40230 AN: 152026 Hom.: 5761 Cov.: 31 AF XY: 0.267 AC XY: 19872 AN XY: 74302

African (AFR) AF: 0.166 AC: 6895 AN: 41476

American (AMR) AF: 0.228 AC: 3486 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3470

East Asian (EAS) AF: 0.418 AC: 2148 AN: 5136

South Asian (SAS) AF: 0.301 AC: 1447 AN: 4800

European-Finnish (FIN) AF: 0.366 AC: 3865 AN: 10560

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20635 AN: 67986

Other (OTH) AF: 0.273 AC: 576 AN: 2112

Alfa AF: 0.164 Hom.: 350

Bravo AF: 0.248

Asia WGS AF: 0.369 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
DANN	Benign	0.38
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2046733;

hg19: chr11-45448090;