2-138002090-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006895.3(HNMT):c.325G>T(p.Glu109*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000502 in 1,592,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_006895.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HNMT | NM_006895.3 | c.325G>T | p.Glu109* | stop_gained | Exon 4 of 6 | ENST00000280097.5 | NP_008826.1 | |
HNMT | XM_017003948.2 | c.223G>T | p.Glu75* | stop_gained | Exon 4 of 6 | XP_016859437.1 | ||
HNMT | XM_017003949.3 | c.325G>T | p.Glu109* | stop_gained | Exon 4 of 5 | XP_016859438.1 | ||
HNMT | XM_011511064.3 | c.-54G>T | 5_prime_UTR_variant | Exon 3 of 5 | XP_011509366.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNMT | ENST00000280097.5 | c.325G>T | p.Glu109* | stop_gained | Exon 4 of 6 | 1 | NM_006895.3 | ENSP00000280097.3 | ||
HNMT | ENST00000410115.5 | c.325G>T | p.Glu109* | stop_gained | Exon 5 of 7 | 5 | ENSP00000386940.1 | |||
HNMT | ENST00000467390.5 | n.337G>T | non_coding_transcript_exon_variant | Exon 4 of 5 | 2 | |||||
HNMT | ENST00000485653.1 | n.257G>T | non_coding_transcript_exon_variant | Exon 3 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152022Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000125 AC: 3AN: 239066Hom.: 0 AF XY: 0.0000232 AC XY: 3AN XY: 129264
GnomAD4 exome AF: 0.00000416 AC: 6AN: 1440928Hom.: 0 Cov.: 29 AF XY: 0.00000279 AC XY: 2AN XY: 716212
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152022Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74244
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at