NM_152269.5:c.44G>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_152269.5(MTRFR):c.44G>A(p.Arg15Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 1,614,092 control chromosomes in the GnomAD database, including 465 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_152269.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0175 AC: 2654AN: 152092Hom.: 41 Cov.: 31
GnomAD3 exomes AF: 0.0189 AC: 4745AN: 251430Hom.: 67 AF XY: 0.0192 AC XY: 2615AN XY: 135896
GnomAD4 exome AF: 0.0218 AC: 31863AN: 1461882Hom.: 424 Cov.: 31 AF XY: 0.0215 AC XY: 15656AN XY: 727240
GnomAD4 genome AF: 0.0174 AC: 2654AN: 152210Hom.: 41 Cov.: 31 AF XY: 0.0167 AC XY: 1245AN XY: 74420
ClinVar
Submissions by phenotype
not specified Benign:3
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
- -
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. -
not provided Benign:2
- -
- -
Spastic paraplegia;C3150801:Combined oxidative phosphorylation defect type 7 Benign:1
- -
Hereditary spastic paraplegia Benign:1
- -
Combined oxidative phosphorylation defect type 7 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at