5-112707527-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001407446.1(APC):c.-191T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,178 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 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APC | NM_001407446.1 | c.-191T>A | 5_prime_UTR_variant | Exon 1 of 16 | NP_001394375.1 | |||
APC | NM_001407447.1 | c.-374T>A | 5_prime_UTR_variant | Exon 1 of 17 | NP_001394376.1 | |||
APC | NM_001407448.1 | c.-141T>A | 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.-141T>A | 5_prime_UTR_variant | Exon 1 of 16 | 4 | ENSP00000426541.2 | ||||
APC | ENST00000507379 | c.-191T>A | 5_prime_UTR_variant | Exon 1 of 14 | 2 | ENSP00000423224.2 | ||||
APC | ENST00000505350.2 | n.-191T>A | non_coding_transcript_exon_variant | Exon 1 of 16 | 3 | ENSP00000481752.1 | ||||
APC | ENST00000505350.2 | n.-191T>A | 5_prime_UTR_variant | Exon 1 of 16 | 3 | ENSP00000481752.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 5
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74342
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 not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with APC-related conditions. 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