rs762333924
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_000038.6(APC):c.934-17del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000731 in 1,613,280 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00037 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000042 ( 0 hom. )
Consequence
APC
NM_000038.6 intron
NM_000038.6 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.64
Genes affected
APC (HGNC:583): (APC regulator of WNT signaling pathway) This gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. It is also involved in other processes including cell migration and adhesion, transcriptional activation, and apoptosis. Defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Mutations in the APC gene have been found to occur in most colorectal cancers, where disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. [provided by RefSeq, Jun 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP6
?
Variant 5-112818946-TA-T is Benign according to our data. Variant chr5-112818946-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 490378.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd4 at 57 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APC | NM_000038.6 | c.934-17del | intron_variant | ENST00000257430.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APC | ENST00000257430.9 | c.934-17del | intron_variant | 5 | NM_000038.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000375 AC: 57AN: 152084Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000998 AC: 25AN: 250570Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135440
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GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461196Hom.: 0 Cov.: 33 AF XY: 0.0000399 AC XY: 29AN XY: 726930
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GnomAD4 genome ? AF: 0.000375 AC: 57AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74300
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 17, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2015 | This variant is associated with the following publications: (PMID: 23159591) - |
Familial adenomatous polyposis 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Mar 28, 2017 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at