20-57564347-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002591.4(PCK1):c.1140T>A(p.Gly380=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G380G) has been classified as Benign.
Frequency
Consequence
NM_002591.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCK1 | NM_002591.4 | c.1140T>A | p.Gly380= | synonymous_variant | 7/10 | ENST00000319441.6 | |
PCK1 | XM_024451888.2 | c.744T>A | p.Gly248= | synonymous_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCK1 | ENST00000319441.6 | c.1140T>A | p.Gly380= | synonymous_variant | 7/10 | 1 | NM_002591.4 | P1 | |
PCK1 | ENST00000467047.1 | n.3268T>A | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
PCK1 | ENST00000485958.1 | n.264T>A | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152038Hom.: 0 Cov.: 31 FAILED QC
GnomAD4 exome Cov.: 51
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152038Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74260
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at