2-177392936-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_003659.4(AGPS):c.147C>T(p.Pro49=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0132 in 1,550,112 control chromosomes in the GnomAD database, including 179 homozygotes. 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. P49P) has been classified as Likely benign.
Frequency
Consequence
NM_003659.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGPS | NM_003659.4 | c.147C>T | p.Pro49= | synonymous_variant | 1/20 | ENST00000264167.11 | |
AGPS | XM_047446105.1 | c.147C>T | p.Pro49= | synonymous_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGPS | ENST00000264167.11 | c.147C>T | p.Pro49= | synonymous_variant | 1/20 | 1 | NM_003659.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00991 AC: 1508AN: 152136Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00974 AC: 1418AN: 145596Hom.: 23 AF XY: 0.00970 AC XY: 762AN XY: 78546
GnomAD4 exome AF: 0.0135 AC: 18932AN: 1397858Hom.: 169 Cov.: 32 AF XY: 0.0132 AC XY: 9129AN XY: 689502
GnomAD4 genome AF: 0.00990 AC: 1508AN: 152254Hom.: 10 Cov.: 32 AF XY: 0.00987 AC XY: 735AN XY: 74434
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 14, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 28, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 05, 2016 | 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. - |
Rhizomelic chondrodysplasia punctata type 3 Benign:3
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Pars Genome Lab | May 18, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jul 12, 2017 | - - |
Rhizomelic chondrodysplasia punctata Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 22, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at