chr15-65003103-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_139242.4(MTFMT):āc.1129A>Cā(p.Lys377Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00173 in 1,610,146 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_139242.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTFMT | ENST00000220058.9 | c.1129A>C | p.Lys377Gln | missense_variant | 9/9 | 1 | NM_139242.4 | ENSP00000220058.4 | ||
MTFMT | ENST00000558460.5 | n.1129A>C | non_coding_transcript_exon_variant | 9/10 | 5 | ENSP00000452646.1 | ||||
MTFMT | ENST00000560717.5 | n.*599A>C | non_coding_transcript_exon_variant | 8/8 | 5 | ENSP00000457257.1 | ||||
MTFMT | ENST00000560717.5 | n.*599A>C | 3_prime_UTR_variant | 8/8 | 5 | ENSP00000457257.1 |
Frequencies
GnomAD3 genomes AF: 0.00105 AC: 160AN: 152178Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000893 AC: 221AN: 247374Hom.: 0 AF XY: 0.000968 AC XY: 130AN XY: 134230
GnomAD4 exome AF: 0.00180 AC: 2623AN: 1457850Hom.: 1 Cov.: 31 AF XY: 0.00176 AC XY: 1274AN XY: 724950
GnomAD4 genome AF: 0.00105 AC: 160AN: 152296Hom.: 1 Cov.: 31 AF XY: 0.00109 AC XY: 81AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | MTFMT: BP4 - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2025 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 22, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at