rs113978322
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The ENST00000433931.7(SYNJ1):c.4252A>G(p.Ile1418Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000224 in 1,613,528 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000433931.7 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 | UniProt |
---|---|---|---|---|---|---|---|
SYNJ1 | NM_203446.3 | c.*223A>G | 3_prime_UTR_variant | 33/33 | ENST00000674351.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNJ1 | ENST00000674351.1 | c.*223A>G | 3_prime_UTR_variant | 33/33 | NM_203446.3 |
Frequencies
GnomAD3 genomes ? AF: 0.00128 AC: 194AN: 151532Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000304 AC: 76AN: 250222Hom.: 0 AF XY: 0.000222 AC XY: 30AN XY: 135290
GnomAD4 exome AF: 0.000111 AC: 162AN: 1461878Hom.: 3 Cov.: 30 AF XY: 0.0000825 AC XY: 60AN XY: 727240
GnomAD4 genome ? AF: 0.00132 AC: 200AN: 151650Hom.: 2 Cov.: 33 AF XY: 0.00130 AC XY: 96AN XY: 74110
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 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 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at