5-112707443-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001407446.1(APC):c.-275A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000046 in 152,292 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 Uncertain significance (★).
Frequency
Consequence
NM_001407446.1 upstream_gene
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APC | ENST00000509732.6 | c.-225A>G | upstream_gene_variant | 4 | ENSP00000426541.2 | |||||
APC | ENST00000507379.6 | c.-275A>G | upstream_gene_variant | 2 | ENSP00000423224.2 | |||||
APC | ENST00000505350.2 | n.-275A>G | upstream_gene_variant | 3 | ENSP00000481752.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152292Hom.: 0 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 255956Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132408
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74410
ClinVar
Submissions by phenotype
Familial adenomatous polyposis 1 Uncertain:1
This variant occurs in a non-coding region of the APC gene. It does not change the encoded amino acid sequence of the APC protein. This variant is present in population databases (no rsID available, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with APC-related conditions. ClinVar contains an entry for this variant (Variation ID: 537604). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at