rs1144098
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005215.4(DCC):c.92-151639A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,088 control chromosomes in the GnomAD database, including 11,679 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.39 ( 11679 hom., cov: 33)
Consequence
DCC
NM_005215.4 intron
NM_005215.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.625
Publications
1 publications found
Genes affected
DCC (HGNC:2701): (DCC netrin 1 receptor) This gene encodes a netrin 1 receptor. The transmembrane protein is a member of the immunoglobulin superfamily of cell adhesion molecules, and mediates axon guidance of neuronal growth cones towards sources of netrin 1 ligand. The cytoplasmic tail interacts with the tyrosine kinases Src and focal adhesion kinase (FAK, also known as PTK2) to mediate axon attraction. The protein partially localizes to lipid rafts, and induces apoptosis in the absence of ligand. The protein functions as a tumor suppressor, and is frequently mutated or downregulated in colorectal cancer and esophageal carcinoma. [provided by RefSeq, Oct 2009]
DCC Gene-Disease associations (from GenCC):
- mirror movements 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Illumina, Ambry Genetics
- mirror movements 1 and/or agenesis of the corpus callosumInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- gaze palsy, familial horizontal, with progressive scoliosis, 2Inheritance: AR Classification: STRONG, LIMITED Submitted by: G2P, Ambry Genetics
- connective tissue disorderInheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
- familial congenital mirror movementsInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Kallmann syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- colorectal cancerInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
- esophageal cancerInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCC | NM_005215.4 | c.92-151639A>G | intron_variant | Intron 1 of 28 | ENST00000442544.7 | NP_005206.2 | ||
DCC | XM_017025568.2 | c.92-151639A>G | intron_variant | Intron 1 of 28 | XP_016881057.1 | |||
DCC | XM_017025569.2 | c.92-151639A>G | intron_variant | Intron 1 of 28 | XP_016881058.1 | |||
DCC | XM_047437311.1 | c.92-151639A>G | intron_variant | Intron 1 of 28 | XP_047293267.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.390 AC: 59315AN: 151970Hom.: 11671 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
59315
AN:
151970
Hom.:
Cov.:
33
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.390 AC: 59337AN: 152088Hom.: 11679 Cov.: 33 AF XY: 0.385 AC XY: 28619AN XY: 74354 show subpopulations
GnomAD4 genome
AF:
AC:
59337
AN:
152088
Hom.:
Cov.:
33
AF XY:
AC XY:
28619
AN XY:
74354
show subpopulations
African (AFR)
AF:
AC:
17573
AN:
41488
American (AMR)
AF:
AC:
5518
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
1438
AN:
3472
East Asian (EAS)
AF:
AC:
1972
AN:
5172
South Asian (SAS)
AF:
AC:
1742
AN:
4820
European-Finnish (FIN)
AF:
AC:
3235
AN:
10566
Middle Eastern (MID)
AF:
AC:
117
AN:
294
European-Non Finnish (NFE)
AF:
AC:
26409
AN:
67986
Other (OTH)
AF:
AC:
867
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1897
3794
5691
7588
9485
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
574
1148
1722
2296
2870
<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:
1300
AN:
3478
ClinVar
Not reported inComputational 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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