chr5-112738572-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000038.6(APC):c.-19+647A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 864,816 control chromosomes in the GnomAD database, including 103,676 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.40 ( 14756 hom., cov: 32)
Exomes 𝑓: 0.50 ( 88920 hom. )
Consequence
APC
NM_000038.6 intron
NM_000038.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.408
Publications
8 publications found
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]
APC Gene-Disease associations (from GenCC):
- classic or attenuated familial adenomatous polyposisInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- desmoid tumorInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Genomics England PanelApp
- familial adenomatous polyposis 1Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics
- gastric adenocarcinoma and proximal polyposis of the stomachInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen, Orphanet
- sarcomaInheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
- APC-related attenuated familial adenomatous polyposisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Turcot syndrome with polyposisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Cenani-Lenz syndactyly syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
Variant 5-112738572-A-G is Benign according to our data. Variant chr5-112738572-A-G is described in ClinVar as Benign. ClinVar VariationId is 82742.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.402 AC: 61025AN: 151952Hom.: 14751 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
61025
AN:
151952
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.496 AC: 353236AN: 712744Hom.: 88920 AF XY: 0.496 AC XY: 164420AN XY: 331398 show subpopulations
GnomAD4 exome
AF:
AC:
353236
AN:
712744
Hom.:
AF XY:
AC XY:
164420
AN XY:
331398
show subpopulations
African (AFR)
AF:
AC:
1274
AN:
13236
American (AMR)
AF:
AC:
490
AN:
826
Ashkenazi Jewish (ASJ)
AF:
AC:
2050
AN:
4354
East Asian (EAS)
AF:
AC:
2041
AN:
3064
South Asian (SAS)
AF:
AC:
7604
AN:
14122
European-Finnish (FIN)
AF:
AC:
128
AN:
272
Middle Eastern (MID)
AF:
AC:
591
AN:
1386
European-Non Finnish (NFE)
AF:
AC:
327606
AN:
652216
Other (OTH)
AF:
AC:
11452
AN:
23268
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.509
Heterozygous variant carriers
0
8140
16279
24419
32558
40698
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
12996
25992
38988
51984
64980
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.401 AC: 61035AN: 152072Hom.: 14756 Cov.: 32 AF XY: 0.405 AC XY: 30092AN XY: 74332 show subpopulations
GnomAD4 genome
AF:
AC:
61035
AN:
152072
Hom.:
Cov.:
32
AF XY:
AC XY:
30092
AN XY:
74332
show subpopulations
African (AFR)
AF:
AC:
5280
AN:
41514
American (AMR)
AF:
AC:
8683
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
1672
AN:
3466
East Asian (EAS)
AF:
AC:
3434
AN:
5152
South Asian (SAS)
AF:
AC:
2654
AN:
4824
European-Finnish (FIN)
AF:
AC:
4336
AN:
10562
Middle Eastern (MID)
AF:
AC:
130
AN:
294
European-Non Finnish (NFE)
AF:
AC:
33452
AN:
67958
Other (OTH)
AF:
AC:
930
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1659
3319
4978
6638
8297
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
570
1140
1710
2280
2850
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1977
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 16, 2022
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Familial colorectal cancer Other:1
-
Systems Biology Platform Zhejiang California International NanoSystems Institute
Significance:other
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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