9-35091718-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_032634.4(PIGO):c.2169G>A(p.Ser723=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,612,038 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 (★★). Synonymous variant affecting the same amino acid position (i.e. S723S) has been classified as Likely benign.
Frequency
Consequence
NM_032634.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGO | NM_032634.4 | c.2169G>A | p.Ser723= | synonymous_variant | 7/11 | ENST00000378617.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGO | ENST00000378617.4 | c.2169G>A | p.Ser723= | synonymous_variant | 7/11 | 1 | NM_032634.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000773 AC: 19AN: 245758Hom.: 0 AF XY: 0.0000448 AC XY: 6AN XY: 133912
GnomAD4 exome AF: 0.0000678 AC: 99AN: 1459848Hom.: 0 Cov.: 31 AF XY: 0.0000565 AC XY: 41AN XY: 726294
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74354
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 14, 2021 | - - |
Hyperphosphatasia with intellectual disability syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at