chr13-27920303-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_000209.4(PDX1):c.165C>A(p.Gly55=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000885 in 1,537,288 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. G55G) has been classified as Likely benign.
Frequency
Consequence
NM_000209.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDX1 | NM_000209.4 | c.165C>A | p.Gly55= | synonymous_variant | 1/2 | ENST00000381033.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDX1 | ENST00000381033.5 | c.165C>A | p.Gly55= | synonymous_variant | 1/2 | 1 | NM_000209.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000769 AC: 117AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000718 AC: 94AN: 130984Hom.: 0 AF XY: 0.000729 AC XY: 52AN XY: 71330
GnomAD4 exome AF: 0.000898 AC: 1244AN: 1384996Hom.: 0 Cov.: 33 AF XY: 0.000903 AC XY: 616AN XY: 682544
GnomAD4 genome AF: 0.000768 AC: 117AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.000819 AC XY: 61AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 23, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 15, 2017 | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 08, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 16, 2020 | - - |
Maturity onset diabetes mellitus in young Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at