rs190326008
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The 5-112707477-A-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000477 in 419,574 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 Benign (★).
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000037 ( 0 hom. )
Consequence
APC
NM_001407446.1 upstream_gene
NM_001407446.1 upstream_gene
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.19
Genes affected
APC (HGNC:583): (APC regulator of WNT signaling pathway) This gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. It is also involved in other processes including cell migration and adhesion, transcriptional activation, and apoptosis. Defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Mutations in the APC gene have been found to occur in most colorectal cancers, where disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. [provided by RefSeq, Jun 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 5-112707477-A-C is Benign according to our data. Variant chr5-112707477-A-C is described in ClinVar as [Benign]. Clinvar id is 469867.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APC | NM_001127511.3 | upstream_gene_variant | |||||
APC | NM_001354895.2 | upstream_gene_variant | |||||
APC | NM_001354897.2 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APC | ENST00000507379.6 | upstream_gene_variant | 2 | ||||||
APC | ENST00000509732.6 | upstream_gene_variant | 4 | P1 | |||||
APC | ENST00000505350.2 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000670 AC: 1AN: 149182Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000370 AC: 1AN: 270392Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0AN XY: 140454
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GnomAD4 genome ? AF: 0.00000670 AC: 1AN: 149182Hom.: 0 Cov.: 33 AF XY: 0.0000137 AC XY: 1AN XY: 72896
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial adenomatous polyposis 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at