rs747129987
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001127178.3(PIGG):āc.711C>Gā(p.Ser237Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000657 in 1,613,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S237N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001127178.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGG | NM_001127178.3 | c.711C>G | p.Ser237Arg | missense_variant | 4/13 | ENST00000453061.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGG | ENST00000453061.7 | c.711C>G | p.Ser237Arg | missense_variant | 4/13 | 1 | NM_001127178.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152038Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000163 AC: 41AN: 250992Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135698
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461686Hom.: 0 Cov.: 31 AF XY: 0.0000633 AC XY: 46AN XY: 727138
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152038Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74268
ClinVar
Submissions by phenotype
Intellectual disability, autosomal recessive 53 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at