chr12-123253667-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_152269.5(MTRFR):c.-8C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 1,614,164 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_152269.5 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTRFR | ENST00000253233 | c.-8C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 3 | 1 | NM_152269.5 | ENSP00000253233.1 | |||
MTRFR | ENST00000253233 | c.-8C>T | 5_prime_UTR_variant | Exon 2 of 3 | 1 | NM_152269.5 | ENSP00000253233.1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152192Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000362 AC: 91AN: 251320Hom.: 0 AF XY: 0.000471 AC XY: 64AN XY: 135852
GnomAD4 exome AF: 0.000163 AC: 238AN: 1461854Hom.: 1 Cov.: 30 AF XY: 0.000235 AC XY: 171AN XY: 727236
GnomAD4 genome AF: 0.000125 AC: 19AN: 152310Hom.: 0 Cov.: 31 AF XY: 0.000175 AC XY: 13AN XY: 74482
ClinVar
Submissions by phenotype
MTRFR-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at