rs114942253
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_203446.3(SYNJ1):c.1030G>A(p.Ala344Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000494 in 1,613,114 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_203446.3 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 |
---|---|---|---|---|---|---|---|
SYNJ1 | NM_203446.3 | c.1030G>A | p.Ala344Thr | missense_variant | 9/33 | ENST00000674351.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNJ1 | ENST00000674351.1 | c.1030G>A | p.Ala344Thr | missense_variant | 9/33 | NM_203446.3 |
Frequencies
GnomAD3 genomes ? AF: 0.00241 AC: 366AN: 152140Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000594 AC: 149AN: 250734Hom.: 1 AF XY: 0.000457 AC XY: 62AN XY: 135544
GnomAD4 exome AF: 0.000294 AC: 430AN: 1460858Hom.: 2 Cov.: 30 AF XY: 0.000266 AC XY: 193AN XY: 726762
GnomAD4 genome ? AF: 0.00241 AC: 367AN: 152256Hom.: 1 Cov.: 32 AF XY: 0.00234 AC XY: 174AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | SYNJ1: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 05, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 18, 2021 | This variant is associated with the following publications: (PMID: 32557143, 27393345) - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2022 | 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. - |
Early-onset Parkinson disease 20;C4479313:Developmental and epileptic encephalopathy, 53 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
SYNJ1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 27, 2022 | 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