2-137970170-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_006895.3(HNMT):c.143G>C(p.Gly48Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000121 in 1,565,764 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. G48G) has been classified as Likely benign.
Frequency
Consequence
NM_006895.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNMT | NM_006895.3 | c.143G>C | p.Gly48Ala | missense_variant | 2/6 | ENST00000280097.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNMT | ENST00000280097.5 | c.143G>C | p.Gly48Ala | missense_variant | 2/6 | 1 | NM_006895.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000416 AC: 1AN: 240384Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 129834
GnomAD4 exome AF: 0.00000637 AC: 9AN: 1413636Hom.: 0 Cov.: 23 AF XY: 0.00000284 AC XY: 2AN XY: 704928
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74324
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | Nov 02, 2023 | PM2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at