2-172063828-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_199227.3(METAP1D):c.316C>T(p.His106Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000031 in 1,613,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_199227.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
METAP1D | ENST00000315796.5 | c.316C>T | p.His106Tyr | missense_variant | Exon 3 of 10 | 1 | NM_199227.3 | ENSP00000315152.4 | ||
METAP1D | ENST00000488581.5 | n.201C>T | non_coding_transcript_exon_variant | Exon 2 of 7 | 3 | |||||
METAP1D | ENST00000493035.5 | n.343C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
METAP1D | ENST00000491440.1 | n.*78C>T | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250784Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135538
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461392Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726972
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.316C>T (p.H106Y) alteration is located in exon 3 (coding exon 3) of the METAP1D gene. This alteration results from a C to T substitution at nucleotide position 316, causing the histidine (H) at amino acid position 106 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