rs35691189
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM1BP4_StrongBS1BS2
The NM_005215.4(DCC):āc.2105A>Gā(p.Asn702Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00402 in 1,610,312 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005215.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCC | ENST00000442544.7 | c.2105A>G | p.Asn702Ser | missense_variant | Exon 14 of 29 | 1 | NM_005215.4 | ENSP00000389140.2 | ||
DCC | ENST00000581580.5 | c.1070A>G | p.Asn357Ser | missense_variant | Exon 11 of 27 | 1 | ENSP00000464582.1 | |||
DCC | ENST00000304775.12 | n.1904A>G | non_coding_transcript_exon_variant | Exon 13 of 19 | 1 | ENSP00000304146.8 |
Frequencies
GnomAD3 genomes AF: 0.00272 AC: 414AN: 152212Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00279 AC: 702AN: 251308Hom.: 1 AF XY: 0.00283 AC XY: 384AN XY: 135806
GnomAD4 exome AF: 0.00415 AC: 6055AN: 1457982Hom.: 19 Cov.: 28 AF XY: 0.00400 AC XY: 2905AN XY: 725676
GnomAD4 genome AF: 0.00272 AC: 414AN: 152330Hom.: 4 Cov.: 32 AF XY: 0.00248 AC XY: 185AN XY: 74486
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
DCC: BS2 -
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Reported in an individual with congenital mirror movements (Meneret et al., 2014); This variant is associated with the following publications: (PMID: 29366874, 24808016) -
Mirror movements 1 Uncertain:1Other:1
May be associated with a higher risk of CMM. -
- -
not specified Benign:1
- -
DCC-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at