rs161870
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002454.3(MTRR):c.537T>C(p.Leu179Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,613,688 control chromosomes in the GnomAD database, including 20,659 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002454.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.206 AC: 31265AN: 151714Hom.: 4518 Cov.: 31
GnomAD3 exomes AF: 0.176 AC: 44201AN: 251326Hom.: 5482 AF XY: 0.163 AC XY: 22109AN XY: 135844
GnomAD4 exome AF: 0.133 AC: 193954AN: 1461856Hom.: 16127 Cov.: 35 AF XY: 0.131 AC XY: 95368AN XY: 727220
GnomAD4 genome AF: 0.206 AC: 31329AN: 151832Hom.: 4532 Cov.: 31 AF XY: 0.204 AC XY: 15159AN XY: 74198
ClinVar
Submissions by phenotype
Methylcobalamin deficiency type cblE Benign:4
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not specified Benign:2
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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. -
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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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at