4-98995824-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015143.3(METAP1):c.71C>G(p.Thr24Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000216 in 1,391,978 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015143.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
METAP1 | NM_015143.3 | c.71C>G | p.Thr24Ser | missense_variant | Exon 1 of 11 | ENST00000296411.11 | NP_055958.2 | |
METAP1 | XM_011531779.3 | c.71C>G | p.Thr24Ser | missense_variant | Exon 1 of 10 | XP_011530081.1 | ||
METAP1 | XM_017007914.3 | c.71C>G | p.Thr24Ser | missense_variant | Exon 1 of 10 | XP_016863403.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000682 AC: 1AN: 146528Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 78298
GnomAD4 exome AF: 0.00000216 AC: 3AN: 1391978Hom.: 0 Cov.: 31 AF XY: 0.00000146 AC XY: 1AN XY: 686694
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.71C>G (p.T24S) alteration is located in exon 1 (coding exon 1) of the METAP1 gene. This alteration results from a C to G substitution at nucleotide position 71, causing the threonine (T) at amino acid position 24 to be replaced by a serine (S). 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