rs754914260
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_005215.4(DCC):c.823C>A(p.Arg275=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,034 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
DCC
NM_005215.4 synonymous
NM_005215.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.92
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.22).
BP7
Synonymous conserved (PhyloP=1.92 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| DCC | NM_005215.4 | c.823C>A | p.Arg275= | synonymous_variant | 4/29 | ENST00000442544.7 | NP_005206.2 | |
| DCC | XM_017025568.2 | c.823C>A | p.Arg275= | synonymous_variant | 4/29 | XP_016881057.1 | ||
| DCC | XM_017025569.2 | c.823C>A | p.Arg275= | synonymous_variant | 4/29 | XP_016881058.1 | ||
| DCC | XM_047437311.1 | c.823C>A | p.Arg275= | synonymous_variant | 4/29 | XP_047293267.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| DCC | ENST00000442544.7 | c.823C>A | p.Arg275= | synonymous_variant | 4/29 | 1 | NM_005215.4 | ENSP00000389140 | P1 | |
| DCC | ENST00000304775.12 | c.625C>A | p.Arg209= | synonymous_variant, NMD_transcript_variant | 3/19 | 1 | ENSP00000304146 | |||
| DCC | ENST00000579883.1 | n.34C>A | non_coding_transcript_exon_variant | 1/3 | 4 | |||||
| DCC | ENST00000584710.5 | n.49C>A | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250852Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135570
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461034Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726822
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GnomAD4 genome
GnomAD4 genome
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32
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at