rs7119425

Variant names:

• chr11-130863290-C-T
• rs7119425
• ENST00000533812.6:n.93-524G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000533812.6(LINC02551):​n.93-524G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,038 control chromosomes in the GnomAD database, including 13,503 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 0.42 (13503 hom., cov: 33)
• Consequence: LINC02551 ENST00000533812.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02551	ENST00000533812.6	n.93-524G>A		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63352 AN: 151920 Hom.: 13500 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.417 AC: 63378 AN: 152038 Hom.: 13503 Cov.: 33 AF XY: 0.420 AC XY: 31213 AN XY: 74334

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.403

Alfa AF: 0.446 Hom.: 7925

Bravo AF: 0.416

Asia WGS AF: 0.524 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7119425; hg19: chr11-130733185;