rs7119425

Positions:

• chr11-130863290-C-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02551	ENST00000533812.6	n.93-524G>A		intron_variant, non_coding_transcript_variant		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;