rs149495971
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001195553.2(DCX):c.856G>T(p.Ala286Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000485 in 1,210,214 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 191 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001195553.2 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 | UniProt |
---|---|---|---|---|---|---|---|
DCX | NM_001195553.2 | c.856G>T | p.Ala286Ser | missense_variant | 5/7 | ENST00000636035.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCX | ENST00000636035.2 | c.856G>T | p.Ala286Ser | missense_variant | 5/7 | 2 | NM_001195553.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000330 AC: 37AN: 112200Hom.: 0 Cov.: 23 AF XY: 0.000291 AC XY: 10AN XY: 34370
GnomAD3 exomes AF: 0.000399 AC: 73AN: 182964Hom.: 0 AF XY: 0.000474 AC XY: 32AN XY: 67552
GnomAD4 exome AF: 0.000501 AC: 550AN: 1097965Hom.: 0 Cov.: 31 AF XY: 0.000498 AC XY: 181AN XY: 363355
GnomAD4 genome ? AF: 0.000330 AC: 37AN: 112249Hom.: 0 Cov.: 23 AF XY: 0.000290 AC XY: 10AN XY: 34429
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 07, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 14, 2015 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | DCX: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2017 | This alteration is classified as 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at