1-25823669-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001099625.2(MTFR1L):c.50C>T(p.Pro17Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000151 in 1,613,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001099625.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTFR1L | NM_001099625.2 | c.50C>T | p.Pro17Leu | missense_variant | Exon 3 of 7 | ENST00000374303.7 | NP_001093095.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTFR1L | ENST00000374303.7 | c.50C>T | p.Pro17Leu | missense_variant | Exon 3 of 7 | 1 | NM_001099625.2 | ENSP00000363421.2 | ||
ENSG00000255054 | ENST00000527604.1 | n.*127C>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 | ENSP00000457066.1 | ||||
ENSG00000255054 | ENST00000527604.1 | n.*127C>T | 3_prime_UTR_variant | Exon 4 of 4 | 5 | ENSP00000457066.1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 249502Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135368
GnomAD4 exome AF: 0.000157 AC: 230AN: 1461790Hom.: 0 Cov.: 31 AF XY: 0.000144 AC XY: 105AN XY: 727198
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.50C>T (p.P17L) alteration is located in exon 3 (coding exon 2) of the MTFR1L gene. This alteration results from a C to T substitution at nucleotide position 50, causing the proline (P) at amino acid position 17 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at