chr5-7870860-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002454.3(MTRR):āc.66A>Gā(p.Ile22Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 1,613,968 control chromosomes in the GnomAD database, including 229,509 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_002454.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.451 AC: 68524AN: 152052Hom.: 16801 Cov.: 34
GnomAD3 exomes AF: 0.466 AC: 117132AN: 251460Hom.: 29891 AF XY: 0.482 AC XY: 65443AN XY: 135902
GnomAD4 exome AF: 0.532 AC: 777894AN: 1461798Hom.: 212709 Cov.: 50 AF XY: 0.534 AC XY: 387990AN XY: 727196
GnomAD4 genome AF: 0.450 AC: 68539AN: 152170Hom.: 16800 Cov.: 34 AF XY: 0.452 AC XY: 33597AN XY: 74408
ClinVar
Submissions by phenotype
not specified Benign:5
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Methylcobalamin deficiency type cblE Benign:4
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Gastrointestinal stromal tumor Uncertain:1
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Disorders of Intracellular Cobalamin Metabolism Benign: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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
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Down syndrome, susceptibility to Other:1
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Neural tube defects, folate-sensitive, susceptibility to Other:1
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Methotrexate response Other:1
There was a significant risk of acute kidney injury at 24 hours after methotrexate administration intravenously with MTRR rs1801394 allele A compared to variant allele G (OR (95%CI) = 2.084 (1.001-4.301), p = 0.047. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at