rs35836343
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000263579.5(DCPS):c.677G>A(p.Gly226Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00491 in 1,613,898 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000263579.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCPS | NM_014026.6 | c.677G>A | p.Gly226Asp | missense_variant | 5/6 | ENST00000263579.5 | NP_054745.1 | |
GSEC | NR_033839.1 | n.147-1025C>T | intron_variant, non_coding_transcript_variant | |||||
DCPS | NM_001350236.2 | c.698G>A | p.Gly233Asp | missense_variant | 5/6 | NP_001337165.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCPS | ENST00000263579.5 | c.677G>A | p.Gly226Asp | missense_variant | 5/6 | 1 | NM_014026.6 | ENSP00000263579 | P1 | |
GSEC | ENST00000629441.3 | n.147-1025C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00400 AC: 609AN: 152124Hom.: 9 Cov.: 31
GnomAD3 exomes AF: 0.00447 AC: 1121AN: 250816Hom.: 6 AF XY: 0.00441 AC XY: 598AN XY: 135626
GnomAD4 exome AF: 0.00500 AC: 7313AN: 1461656Hom.: 31 Cov.: 32 AF XY: 0.00505 AC XY: 3673AN XY: 727110
GnomAD4 genome AF: 0.00400 AC: 609AN: 152242Hom.: 9 Cov.: 31 AF XY: 0.00356 AC XY: 265AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2024 | DCPS: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jul 13, 2016 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 18, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Al-Raqad syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
DCPS-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 07, 2020 | This variant is classified as 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