rs548146

Variant names:

• chr11-111165332-A-G
• rs548146
• ENST00000636877.1:n.837+4931T>C

Variant summary

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

The ENST00000636877.1(LINC02550):​n.837+4931T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,898 control chromosomes in the GnomAD database, including 11,244 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 0.38 (11244 hom., cov: 32)
• Consequence: LINC02550 ENST00000636877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

LINC02550 (HGNC:53585): (long intergenic non-protein coding RNA 2550)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.459 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
LINC02550	ENST00000636877.1	n.837+4931T>C		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57402 AN: 151780 Hom.: 11205 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.378 AC: 57482 AN: 151898 Hom.: 11244 Cov.: 32 AF XY: 0.379 AC XY: 28104 AN XY: 74230

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.370

Alfa AF: 0.354 Hom.: 1226

Bravo AF: 0.399

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs548146; hg19: chr11-111036056;