rs77401816
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_006623.4(PHGDH):c.624T>A(p.Pro208=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P208P) has been classified as Benign.
Frequency
Consequence
NM_006623.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHGDH | NM_006623.4 | c.624T>A | p.Pro208= | synonymous_variant | 6/12 | ENST00000641023.2 | NP_006614.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHGDH | ENST00000641023.2 | c.624T>A | p.Pro208= | synonymous_variant | 6/12 | NM_006623.4 | ENSP00000493175 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151896Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151896Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74200
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at