rs747359907
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Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PP5_Very_Strong
The ENST00000454060.2(LINC00571):n.322+171_322+173del 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 0.0000258 in 1,279,514 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000028 ( 0 hom. )
Consequence
LINC00571
ENST00000454060.2 intron, non_coding_transcript
ENST00000454060.2 intron, non_coding_transcript
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.21
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 13-38349764-TTCA-T is Pathogenic according to our data. Variant chr13-38349764-TTCA-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 495149.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-38349764-TTCA-T is described in Lovd as [Pathogenic]. Variant chr13-38349764-TTCA-T is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC00571 | ENST00000454060.2 | n.322+171_322+173del | intron_variant, non_coding_transcript_variant | 3 | |||||
LINC00571 | ENST00000451826.2 | n.322+171_322+173del | intron_variant, non_coding_transcript_variant | 2 | |||||
LINC00571 | ENST00000700975.1 | n.304+171_304+173del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000284 AC: 32AN: 1127316Hom.: 0 AF XY: 0.0000351 AC XY: 20AN XY: 569990
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:13
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Leukodystrophy, hypomyelinating, 14 Pathogenic:10
Pathogenic, criteria provided, single submitter | clinical testing | Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Dec 12, 2023 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 06, 2018 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Laboratory of Medical Genetics, National & Kapodistrian University of Athens | May 09, 2022 | PS3, PM2, PP5 - |
Pathogenic, criteria provided, single submitter | clinical testing | Suma Genomics | - | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego | Sep 30, 2020 | This variant is located in the promoter region of UFM1 and has been previously reported as a homozygous change in sixteen patients with hypomyelination with atrophy of the basal ganglia and cerebellum (PMID: 28931644). Most of the patients were from Roma population, and the carrier frequency was as high as 25% in Eastern Slovakia (PMID: 28931644), suggesting a founder effect. In-vitro functional studies using a luciferase assay showed that this variant leads to reduced promoter activity in CNS-derived cell lines (PMID: 28931644). It is absent from the gnomAD population database and thus is presumed to be rare. Based on the available evidence, the c.-273_-271delTCA variant is classified as Likely Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 21, 2021 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Centogene AG - the Rare Disease Company | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Nov 28, 2018 | This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3. This variant was detected in homozygous state. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Sep 13, 2023 | Criteria applied: PS3,PM3,PM2_SUP - |
not provided Pathogenic:3
Pathogenic, no assertion criteria provided | clinical testing | Molecular Genetics laboratory, Necker Hospital | Apr 16, 2020 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | UFM1: PM3:Very Strong, PM2 - |
Pathogenic, criteria provided, single submitter | clinical testing | Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes | Sep 19, 2018 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at