11-130820267-A-G

Variant names:

• chr11-130820267-A-G
• rs1944146
• ENST00000741042.1:n.347-12033T>C

Variant summary

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

The ENST00000741042.1(LINC02551):​n.347-12033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,176 control chromosomes in the GnomAD database, including 12,685 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 0.40 (12685 hom., cov: 33)
• Consequence: LINC02551 ENST00000741042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 3 publications found

Genes affected

LINC02551 (HGNC:53586): (long intergenic non-protein coding RNA 2551)

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 (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741042.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02551	ENST00000741042.1		n.347-12033T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61168 AN: 152058 Hom.: 12683 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.402 AC: 61201 AN: 152176 Hom.: 12685 Cov.: 33 AF XY: 0.404 AC XY: 30066 AN XY: 74380

African (AFR) AF: 0.320 AC: 13271 AN: 41510

American (AMR) AF: 0.351 AC: 5363 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3472

East Asian (EAS) AF: 0.456 AC: 2359 AN: 5168

South Asian (SAS) AF: 0.383 AC: 1849 AN: 4826

European-Finnish (FIN) AF: 0.487 AC: 5150 AN: 10584

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.443 AC: 30091 AN: 68002

Other (OTH) AF: 0.415 AC: 878 AN: 2116

Alfa AF: 0.406 Hom.: 4982

Bravo AF: 0.389

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.038
DANN	Benign	0.36
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1944146; hg19: chr11-130690162; COSMIC: COSV51305017;