5-112707530-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001407446.1(APC):c.-188C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 487,828 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 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 Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APC | NM_001407446.1 | c.-188C>T | 5_prime_UTR_variant | Exon 1 of 16 | NP_001394375.1 | |||
APC | NM_001407447.1 | c.-371C>T | 5_prime_UTR_variant | Exon 1 of 17 | NP_001394376.1 | |||
APC | NM_001407448.1 | c.-138C>T | 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 | c.-138C>T | 5_prime_UTR_variant | Exon 1 of 16 | 4 | ENSP00000426541.2 | ||||
APC | ENST00000507379 | c.-188C>T | 5_prime_UTR_variant | Exon 1 of 14 | 2 | ENSP00000423224.2 | ||||
APC | ENST00000505350.2 | n.-188C>T | non_coding_transcript_exon_variant | Exon 1 of 16 | 3 | ENSP00000481752.1 | ||||
APC | ENST00000505350.2 | n.-188C>T | 5_prime_UTR_variant | Exon 1 of 16 | 3 | ENSP00000481752.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152250Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000238 AC: 8AN: 335578Hom.: 0 Cov.: 5 AF XY: 0.0000345 AC XY: 6AN XY: 174006
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
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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 (rs761454123, gnomAD 0.01%). 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: 469858). 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. -
not provided Uncertain:1
Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge; Also known as c.-47361C>T; This variant is associated with the following publications: (PMID: 27087319) -
Hereditary cancer-predisposing syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at