rs7943757

chr11-130846262-C-T

Variant summary

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

The NR_125383.1(LINC02551):n.545-71G>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 0.495 in 449,738 control chromosomes in the GnomAD database, including 56,681 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 0.53 (22200 hom., cov: 32)
  • Exomes 𝑓: 0.48 (34481 hom.)
• Consequence: LINC02551 NR_125383.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02551	NR_125383.1	n.545-71G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02551	ENST00000533812.6	n.1293-71G>A		intron_variant, non_coding_transcript_variant		5
LINC02551	ENST00000533434.1	n.233-71G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80420 AN: 151890 Hom.: 22160 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.491

GnomAD4 exome AF: 0.478 AC: 142211 AN: 297730 Hom.: 34481 AF XY: 0.472 AC XY: 80030 AN XY: 169448

Gnomad4 AFR exome AF: 0.686

Gnomad4 AMR exome AF: 0.532

Gnomad4 ASJ exome AF: 0.429

Gnomad4 EAS exome AF: 0.456

Gnomad4 SAS exome AF: 0.464

Gnomad4 FIN exome AF: 0.474

Gnomad4 NFE exome AF: 0.468

Gnomad4 OTH exome AF: 0.479

GnomAD4 genome AF: 0.530 AC: 80511 AN: 152008 Hom.: 22200 Cov.: 32 AF XY: 0.529 AC XY: 39327 AN XY: 74278

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.493

Alfa AF: 0.488 Hom.: 10527

Bravo AF: 0.541

Asia WGS AF: 0.540 AC: 1879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.48
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7943757; hg19: chr11-130716157;