18-52340854-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005215.4(DCC):āc.67T>Cā(p.Phe23Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.986 in 1,613,996 control chromosomes in the GnomAD database, including 784,792 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_005215.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCC | NM_005215.4 | c.67T>C | p.Phe23Leu | missense_variant | 1/29 | ENST00000442544.7 | NP_005206.2 | |
DCC | XM_017025568.2 | c.67T>C | p.Phe23Leu | missense_variant | 1/29 | XP_016881057.1 | ||
DCC | XM_017025569.2 | c.67T>C | p.Phe23Leu | missense_variant | 1/29 | XP_016881058.1 | ||
DCC | XM_047437311.1 | c.67T>C | p.Phe23Leu | missense_variant | 1/29 | XP_047293267.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.986 AC: 150040AN: 152136Hom.: 73999 Cov.: 31
GnomAD3 exomes AF: 0.986 AC: 247863AN: 251496Hom.: 122177 AF XY: 0.986 AC XY: 133985AN XY: 135922
GnomAD4 exome AF: 0.986 AC: 1441364AN: 1461742Hom.: 710734 Cov.: 47 AF XY: 0.986 AC XY: 717200AN XY: 727186
GnomAD4 genome AF: 0.986 AC: 150158AN: 152254Hom.: 74058 Cov.: 31 AF XY: 0.985 AC XY: 73308AN XY: 74430
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Gaze palsy, familial horizontal, with progressive scoliosis, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Mirror movements 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at