chr19-13764725-AGCGGGGCGGCGGGGCGGCGGGGCGGCGGGGCGGCGGGGCG-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001031727.4(MRI1):c.132+48_133-64del variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 1,238,100 control chromosomes in the GnomAD database, including 59,569 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.49 ( 12582 hom., cov: 0)
Exomes 𝑓: 0.11 ( 46987 hom. )
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 19-13764725-AGCGGGGCGGCGGGGCGGCGGGGCGGCGGGGCGGCGGGGCG-A is Benign according to our data. Variant chr19-13764725-AGCGGGGCGGCGGGGCGGCGGGGCGGCGGGGCGGCGGGGCG-A is described in ClinVar as [Likely_benign]. Clinvar id is 1995432.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRI1 | NM_001031727.4 | c.132+48_133-64del | splice_donor_region_variant, intron_variant | ENST00000040663.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRI1 | ENST00000040663.8 | c.132+48_133-64del | splice_donor_region_variant, intron_variant | 1 | NM_001031727.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.485 AC: 54699AN: 112706Hom.: 12575 Cov.: 0
GnomAD3 genomes
AF:
AC:
54699
AN:
112706
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000108 AC: 9AN: 83100Hom.: 4 AF XY: 0.000142 AC XY: 7AN XY: 49186
GnomAD3 exomes
AF:
AC:
9
AN:
83100
Hom.:
AF XY:
AC XY:
7
AN XY:
49186
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.109 AC: 122516AN: 1125314Hom.: 46987 AF XY: 0.118 AC XY: 64501AN XY: 544346
GnomAD4 exome
AF:
AC:
122516
AN:
1125314
Hom.:
AF XY:
AC XY:
64501
AN XY:
544346
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.485 AC: 54727AN: 112786Hom.: 12582 Cov.: 0 AF XY: 0.489 AC XY: 26463AN XY: 54152
GnomAD4 genome
AF:
AC:
54727
AN:
112786
Hom.:
Cov.:
0
AF XY:
AC XY:
26463
AN XY:
54152
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 23, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at