rs1043505718
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001407446.1(APC):c.16G>A(p.Gly6Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000686 in 1,370,660 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G6D) has been classified as Uncertain significance.
Frequency
Consequence
NM_001407446.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APC | NM_001407446.1 | c.16G>A | p.Gly6Ser | missense_variant | 1/16 | ||
APC | NM_001354897.2 | c.16G>A | p.Gly6Ser | missense_variant | 1/15 | ||
APC | NM_001127511.3 | c.16G>A | p.Gly6Ser | missense_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APC | ENST00000507379.6 | c.16G>A | p.Gly6Ser | missense_variant | 1/14 | 2 | |||
APC | ENST00000509732.6 | c.-19+84G>A | intron_variant | 4 | P1 | ||||
APC | ENST00000505350.2 | c.16G>A | p.Gly6Ser | missense_variant, NMD_transcript_variant | 1/16 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000953 AC: 13AN: 136392Hom.: 0 AF XY: 0.0000809 AC XY: 6AN XY: 74140
GnomAD4 exome AF: 0.0000402 AC: 49AN: 1218380Hom.: 0 Cov.: 31 AF XY: 0.0000302 AC XY: 18AN XY: 595232
GnomAD4 genome ? AF: 0.000296 AC: 45AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74456
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 20, 2017 | - - |
Familial adenomatous polyposis 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at