chr2-177392837-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_003659.4(AGPS):c.48C>T(p.Gly16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000188 in 1,546,350 control chromosomes in the GnomAD database, including 1 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. G16G) 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 -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGPS | NM_003659.4 | c.48C>T | p.Gly16= | synonymous_variant | 1/20 | ENST00000264167.11 | |
AGPS | XM_047446105.1 | c.48C>T | p.Gly16= | synonymous_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGPS | ENST00000264167.11 | c.48C>T | p.Gly16= | synonymous_variant | 1/20 | 1 | NM_003659.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152016Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000179 AC: 25AN: 1394334Hom.: 1 Cov.: 32 AF XY: 0.0000160 AC XY: 11AN XY: 689092
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152016Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74248
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at