rs554351451
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_001407446.1(APC):c.-204A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000373 in 461,702 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001407446.1 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APC | NM_001407446.1 | c.-204A>G | 5_prime_UTR_variant | Exon 1 of 16 | NP_001394375.1 | |||
APC | NM_001407447.1 | c.-387A>G | 5_prime_UTR_variant | Exon 1 of 17 | NP_001394376.1 | |||
APC | NM_001407448.1 | c.-154A>G | 5_prime_UTR_variant | Exon 1 of 17 | NP_001394377.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APC | ENST00000509732.6 | c.-154A>G | upstream_gene_variant | 4 | ENSP00000426541.2 | |||||
APC | ENST00000507379.6 | c.-204A>G | upstream_gene_variant | 2 | ENSP00000423224.2 | |||||
APC | ENST00000505350.2 | n.-204A>G | upstream_gene_variant | 3 | ENSP00000481752.1 |
Frequencies
GnomAD3 genomes AF: 0.000717 AC: 109AN: 152078Hom.: 1 Cov.: 33
GnomAD4 exome AF: 0.000204 AC: 63AN: 309506Hom.: 1 Cov.: 4 AF XY: 0.000198 AC XY: 32AN XY: 161262
GnomAD4 genome AF: 0.000716 AC: 109AN: 152196Hom.: 1 Cov.: 33 AF XY: 0.00105 AC XY: 78AN XY: 74402
ClinVar
Submissions by phenotype
Neoplasm of stomach;C0699790:Carcinoma of colon;C1851124:Desmoid disease, hereditary;C2239176:Hepatocellular carcinoma;C2713442:Familial adenomatous polyposis 1 Uncertain:1
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Familial adenomatous polyposis 1 Benign:1
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APC-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at