15-65029598-G-C
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM5BP4_StrongBP6_Very_StrongBS1BS2
The NM_139242.4(MTFMT):āc.16C>Gā(p.Arg6Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000406 in 1,429,532 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R6P) has been classified as Likely pathogenic.
Frequency
Consequence
NM_139242.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTFMT | NM_139242.4 | c.16C>G | p.Arg6Gly | missense_variant | 1/9 | ENST00000220058.9 | NP_640335.2 | |
MTFMT | XM_005254158.6 | c.16C>G | p.Arg6Gly | missense_variant | 1/9 | XP_005254215.2 | ||
MTFMT | XR_001751081.2 | n.42C>G | non_coding_transcript_exon_variant | 1/5 | ||||
MTFMT | XR_007064421.1 | n.42C>G | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00229 AC: 348AN: 151876Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.0000833 AC: 6AN: 72046Hom.: 0 AF XY: 0.0000720 AC XY: 3AN XY: 41690
GnomAD4 exome AF: 0.000180 AC: 230AN: 1277546Hom.: 1 Cov.: 32 AF XY: 0.000157 AC XY: 98AN XY: 625938
GnomAD4 genome AF: 0.00230 AC: 350AN: 151986Hom.: 2 Cov.: 32 AF XY: 0.00227 AC XY: 169AN XY: 74288
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 17, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 13, 2020 | - - |
MTFMT-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 05, 2019 | This variant is classified as 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