rs777188684
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001407446.1(APC):c.22G>A(p.Gly8Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000255 in 1,370,666 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001407446.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APC | NM_001407446.1 | c.22G>A | p.Gly8Ser | missense_variant | Exon 1 of 16 | NP_001394375.1 | ||
APC | NM_001354897.2 | c.22G>A | p.Gly8Ser | missense_variant | Exon 1 of 15 | NP_001341826.1 | ||
APC | NM_001127511.3 | c.22G>A | p.Gly8Ser | missense_variant | Exon 1 of 14 | NP_001120983.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APC | ENST00000507379.6 | c.22G>A | p.Gly8Ser | missense_variant | Exon 1 of 14 | 2 | ENSP00000423224.2 | |||
APC | ENST00000509732.6 | c.-19+90G>A | intron_variant | Intron 1 of 15 | 4 | ENSP00000426541.2 | ||||
APC | ENST00000505350.2 | n.22G>A | non_coding_transcript_exon_variant | Exon 1 of 16 | 3 | ENSP00000481752.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000955 AC: 13AN: 136182Hom.: 1 AF XY: 0.0000946 AC XY: 7AN XY: 74030
GnomAD4 exome AF: 0.0000263 AC: 32AN: 1218376Hom.: 1 Cov.: 31 AF XY: 0.0000336 AC XY: 20AN XY: 595228
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74468
ClinVar
Submissions by phenotype
Familial adenomatous polyposis 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at