chr5-79119262-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001713.3(BHMT):c.170G>T(p.Arg57Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000174 in 1,601,794 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. R57C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001713.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BHMT | NM_001713.3 | c.170G>T | p.Arg57Leu | missense_variant | 3/8 | ENST00000274353.10 | |
LOC124901012 | XR_007058837.1 | n.54C>A | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BHMT | ENST00000274353.10 | c.170G>T | p.Arg57Leu | missense_variant | 3/8 | 1 | NM_001713.3 | P1 | |
BHMT | ENST00000524080.1 | c.166+3363G>T | intron_variant | 2 | |||||
BHMT | ENST00000520703.1 | n.247G>T | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
DMGDH | ENST00000520388.5 | n.491+1079C>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152116Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000113 AC: 27AN: 239876Hom.: 0 AF XY: 0.0000848 AC XY: 11AN XY: 129670
GnomAD4 exome AF: 0.000179 AC: 260AN: 1449678Hom.: 0 Cov.: 29 AF XY: 0.000176 AC XY: 127AN XY: 721024
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152116Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2023 | The c.170G>T (p.R57L) alteration is located in exon 3 (coding exon 3) of the BHMT gene. This alteration results from a G to T substitution at nucleotide position 170, causing the arginine (R) at amino acid position 57 to be replaced by a leucine (L). 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