chr1-37822637-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BP4
The NM_005955.3(MTF1):c.1251A>C(p.Leu417Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,722 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_005955.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTF1 | NM_005955.3 | c.1251A>C | p.Leu417Phe | missense_variant | 9/11 | ENST00000373036.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTF1 | ENST00000373036.5 | c.1251A>C | p.Leu417Phe | missense_variant | 9/11 | 1 | NM_005955.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152026Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461696Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727134
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152026Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2022 | The c.1251A>C (p.L417F) alteration is located in exon 9 (coding exon 8) of the MTF1 gene. This alteration results from a A to C substitution at nucleotide position 1251, causing the leucine (L) at amino acid position 417 to be replaced by a phenylalanine (F). 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