1-236795291-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001291939.1(MTR):c.-413C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000554 in 1,209,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001291939.1 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTR | ENST00000680454.1 | n.32C>A | non_coding_transcript_exon_variant | Exon 1 of 32 | ||||||
MTR | ENST00000366577.10 | c.-413C>A | upstream_gene_variant | 1 | NM_000254.3 | ENSP00000355536.5 | ||||
MTR | ENST00000674797.2 | c.-546C>A | upstream_gene_variant | ENSP00000502299.2 | ||||||
MTR | ENST00000652435.1 | n.-546C>A | upstream_gene_variant | ENSP00000505932.1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000106 AC: 7AN: 65924Hom.: 0 AF XY: 0.000148 AC XY: 5AN XY: 33724
GnomAD4 exome AF: 0.0000539 AC: 57AN: 1056846Hom.: 0 Cov.: 30 AF XY: 0.0000572 AC XY: 29AN XY: 506910
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74378
ClinVar
Submissions by phenotype
Disorders of Intracellular Cobalamin Metabolism Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at