ENST00000636877.1:n.837+4931T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636877.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02550	ENST00000636877.1	TSL:5	n.837+4931T>C		intron	N/A

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

African (AFR) AF: 0.450 AC: 18629 AN: 41414

American (AMR) AF: 0.468 AC: 7147 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3464

East Asian (EAS) AF: 0.353 AC: 1822 AN: 5166

South Asian (SAS) AF: 0.316 AC: 1522 AN: 4810

European-Finnish (FIN) AF: 0.270 AC: 2846 AN: 10524

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.344 AC: 23402 AN: 67938

Other (OTH) AF: 0.370 AC: 782 AN: 2112

Alfa AF: 0.358 Hom.: 2865

Bravo AF: 0.399

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.40
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs548146; hg19: chr11-111036056;