5-79077492-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_017614.5(BHMT2):c.46C>T(p.Arg16Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000317 in 1,611,278 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R16H) has been classified as Uncertain significance.
Frequency
Consequence
NM_017614.5 missense
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 |
---|---|---|---|---|---|---|---|---|
BHMT2 | NM_017614.5 | c.46C>T | p.Arg16Cys | missense_variant | Exon 2 of 8 | ENST00000255192.8 | NP_060084.2 | |
BHMT2 | NM_001178005.2 | c.46C>T | p.Arg16Cys | missense_variant | Exon 2 of 7 | NP_001171476.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000400 AC: 6AN: 149992Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250788Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135582
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461260Hom.: 0 Cov.: 39 AF XY: 0.0000344 AC XY: 25AN XY: 726942
GnomAD4 genome AF: 0.0000400 AC: 6AN: 150018Hom.: 0 Cov.: 31 AF XY: 0.0000274 AC XY: 2AN XY: 73002
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.46C>T (p.R16C) alteration is located in exon 2 (coding exon 2) of the BHMT2 gene. This alteration results from a C to T substitution at nucleotide position 46, causing the arginine (R) at amino acid position 16 to be replaced by a cysteine (C). 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