chr11-111165332-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000636877.1(LINC02550):​n.837+4931T>C 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 0.378 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, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04
Variant links:
Genes affected
LINC02550 (HGNC:53585): (long intergenic non-protein coding RNA 2550)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC02550ENST00000636877.1 linkuse as main transcriptn.837+4931T>C intron_variant, non_coding_transcript_variant 5

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs548146; hg19: chr11-111036056; API