rs75543815
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_000367.5(TPMT):c.539A>T(p.Tyr180Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000949 in 1,611,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000367.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TPMT | NM_000367.5 | c.539A>T | p.Tyr180Phe | missense_variant | 7/9 | ENST00000309983.5 | NP_000358.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPMT | ENST00000309983.5 | c.539A>T | p.Tyr180Phe | missense_variant | 7/9 | 1 | NM_000367.5 | ENSP00000312304 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000932 AC: 14AN: 150180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000195 AC: 49AN: 251380Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135872
GnomAD4 exome AF: 0.0000951 AC: 139AN: 1461630Hom.: 0 Cov.: 33 AF XY: 0.0000908 AC XY: 66AN XY: 727138
GnomAD4 genome AF: 0.0000932 AC: 14AN: 150208Hom.: 0 Cov.: 33 AF XY: 0.000137 AC XY: 10AN XY: 73142
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at