11-130839172-C-T

Variant names:

• chr11-130839172-C-T
• rs7943936
• ENST00000741042.1:n.346+15555G>A

Variant summary

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

The ENST00000741042.1(LINC02551):​n.346+15555G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,998 control chromosomes in the GnomAD database, including 24,065 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 0.56 (24065 hom., cov: 32)
• Consequence: LINC02551 ENST00000741042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 9 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 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.346+15555G>A		intron	N/A
	LINC02551	ENST00000741043.1		n.567+6955G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84595 AN: 151880 Hom.: 24017 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.557 AC: 84697 AN: 151998 Hom.: 24065 Cov.: 32 AF XY: 0.554 AC XY: 41122 AN XY: 74288

African (AFR) AF: 0.673 AC: 27897 AN: 41474

American (AMR) AF: 0.526 AC: 8030 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1781 AN: 3468

East Asian (EAS) AF: 0.599 AC: 3094 AN: 5162

South Asian (SAS) AF: 0.570 AC: 2742 AN: 4812

European-Finnish (FIN) AF: 0.451 AC: 4754 AN: 10548

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34452 AN: 67962

Other (OTH) AF: 0.584 AC: 1232 AN: 2110

Alfa AF: 0.523 Hom.: 93135

Bravo AF: 0.567

Asia WGS AF: 0.548 AC: 1908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.74
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs7943936; hg19: chr11-130709067;