1-25823671-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001099625.2(MTFR1L):c.52C>T(p.His18Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTFR1L | NM_001099625.2 | c.52C>T | p.His18Tyr | 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.52C>T | p.His18Tyr | missense_variant | Exon 3 of 7 | 1 | NM_001099625.2 | ENSP00000363421.2 | ||
ENSG00000255054 | ENST00000527604.1 | n.*129C>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 | ENSP00000457066.1 | ||||
ENSG00000255054 | ENST00000527604.1 | n.*129C>T | 3_prime_UTR_variant | Exon 4 of 4 | 5 | ENSP00000457066.1 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000601 AC: 15AN: 249514Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135372
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461788Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727196
GnomAD4 genome AF: 0.000263 AC: 40AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.52C>T (p.H18Y) 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 52, causing the histidine (H) at amino acid position 18 to be replaced by a tyrosine (Y). 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