5-112707473-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001407446.1(APC):c.-245A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0393 in 417,264 control chromosomes in the GnomAD database, including 681 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001407446.1 upstream_gene
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APC | ENST00000509732.6 | c.-195A>C | upstream_gene_variant | 4 | ENSP00000426541.2 | |||||
APC | ENST00000507379.6 | c.-245A>C | upstream_gene_variant | 2 | ENSP00000423224.2 | |||||
APC | ENST00000505350.2 | n.-245A>C | upstream_gene_variant | 3 | ENSP00000481752.1 |
Frequencies
GnomAD3 genomes AF: 0.0472 AC: 7180AN: 152174Hom.: 328 Cov.: 33
GnomAD4 exome AF: 0.0348 AC: 9219AN: 264972Hom.: 352 Cov.: 2 AF XY: 0.0367 AC XY: 5040AN XY: 137444
GnomAD4 genome AF: 0.0472 AC: 7187AN: 152292Hom.: 329 Cov.: 33 AF XY: 0.0476 AC XY: 3542AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:2
- -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Familial adenomatous polyposis 1 Benign:1
- -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at