chr9-21802762-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_002451.4(MTAP):c.14C>T(p.Thr5Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,612,530 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002451.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTAP | NM_002451.4 | c.14C>T | p.Thr5Ile | missense_variant | 1/8 | ENST00000644715.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTAP | ENST00000644715.2 | c.14C>T | p.Thr5Ile | missense_variant | 1/8 | NM_002451.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151894Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246148Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134110
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460636Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726640
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151894Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 74198
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.14C>T (p.T5I) alteration is located in exon 1 (coding exon 1) of the MTAP gene. This alteration results from a C to T substitution at nucleotide position 14, causing the threonine (T) at amino acid position 5 to be replaced by an isoleucine (I). 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