chr7-134678930-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP4_StrongBP6_Moderate
The NM_001724.5(BPGM):c.679C>T(p.Arg227Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000306 in 1,613,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R227H) has been classified as Likely benign.
Frequency
Consequence
NM_001724.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BPGM | NM_001724.5 | c.679C>T | p.Arg227Cys | missense_variant | 3/3 | ENST00000344924.8 | |
LOC124901750 | XR_007060537.1 | n.29222-58982G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BPGM | ENST00000344924.8 | c.679C>T | p.Arg227Cys | missense_variant | 3/3 | 1 | NM_001724.5 | P1 | |
BPGM | ENST00000393132.2 | c.679C>T | p.Arg227Cys | missense_variant | 4/4 | 5 | P1 | ||
BPGM | ENST00000418040.5 | c.679C>T | p.Arg227Cys | missense_variant | 4/4 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000461 AC: 116AN: 251450Hom.: 0 AF XY: 0.000626 AC XY: 85AN XY: 135888
GnomAD4 exome AF: 0.000312 AC: 456AN: 1461682Hom.: 0 Cov.: 30 AF XY: 0.000410 AC XY: 298AN XY: 727146
GnomAD4 genome AF: 0.000250 AC: 38AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at