chr19-13764725-A-AGCGGGGCG
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001031727.4(MRI1):c.133-71_133-64dup variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0021 ( 1 hom., cov: 0)
Consequence
MRI1
NM_001031727.4 splice_donor_region, intron
NM_001031727.4 splice_donor_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.31
Genes affected
MRI1 (HGNC:28469): (methylthioribose-1-phosphate isomerase 1) This enzyme functions in the methionine salvage pathway by catalyzing the interconversion of methylthioribose-1-phosphate and methythioribulose-1-phosphate. Elevated expression of the encoded protein is associated with metastatic melanoma and this protein promotes melanoma cell invasion independent of its enzymatic activity. Mutations in this gene may be associated with vanishing white matter disease (VMWD). [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
?
Variant 19-13764725-A-AGCGGGGCG is Benign according to our data. Variant chr19-13764725-A-AGCGGGGCG is described in ClinVar as [Benign]. Clinvar id is 2007650.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRI1 | NM_001031727.4 | c.133-71_133-64dup | splice_donor_region_variant, intron_variant | ENST00000040663.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRI1 | ENST00000040663.8 | c.133-71_133-64dup | splice_donor_region_variant, intron_variant | 1 | NM_001031727.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00214 AC: 241AN: 112650Hom.: 1 Cov.: 0
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GnomAD4 genome ? AF: 0.00214 AC: 241AN: 112728Hom.: 1 Cov.: 0 AF XY: 0.00174 AC XY: 94AN XY: 54126
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
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Name
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at