chr5-112707880-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001407446.1(APC):c.163C>G(p.Gln55Glu) variant causes a missense, splice region 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. 2/2 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q55H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001407446.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APC | NM_001407446.1 | c.163C>G | p.Gln55Glu | missense_variant, splice_region_variant | 1/16 | ||
APC | NM_001354897.2 | c.163C>G | p.Gln55Glu | missense_variant, splice_region_variant | 1/15 | ||
APC | NM_001127511.3 | c.163C>G | p.Gln55Glu | missense_variant, splice_region_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APC | ENST00000507379.6 | c.163C>G | p.Gln55Glu | missense_variant, splice_region_variant | 1/14 | 2 | |||
APC | ENST00000509732.6 | c.-19+231C>G | intron_variant | 4 | P1 | ||||
APC | ENST00000505350.2 | c.163C>G | p.Gln55Glu | missense_variant, splice_region_variant, NMD_transcript_variant | 1/16 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.