3-129061838-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000174.5(GP9):c.99G>T(p.Gly33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,198 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. G33G) has been classified as Likely benign.
Frequency
Consequence
NM_000174.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GP9 | NM_000174.5 | c.99G>T | p.Gly33= | synonymous_variant | 3/3 | ENST00000307395.5 | |
GP9 | XM_047447997.1 | c.99G>T | p.Gly33= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GP9 | ENST00000307395.5 | c.99G>T | p.Gly33= | synonymous_variant | 3/3 | 1 | NM_000174.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000412 AC: 1AN: 242832Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132156
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460198Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726368
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at