chrX-49191511-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003179.3(SYP):c.868G>T(p.Gly290Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,210,117 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 67 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G290E) has been classified as Likely benign.
Frequency
Consequence
NM_003179.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYP | NM_003179.3 | c.868G>T | p.Gly290Trp | missense_variant | 6/7 | ENST00000263233.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYP | ENST00000263233.9 | c.868G>T | p.Gly290Trp | missense_variant | 6/7 | 1 | NM_003179.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000203 AC: 23AN: 113041Hom.: 0 Cov.: 24 AF XY: 0.000171 AC XY: 6AN XY: 35173
GnomAD3 exomes AF: 0.000334 AC: 59AN: 176549Hom.: 0 AF XY: 0.000186 AC XY: 12AN XY: 64377
GnomAD4 exome AF: 0.000173 AC: 190AN: 1097023Hom.: 0 Cov.: 31 AF XY: 0.000168 AC XY: 61AN XY: 362809
GnomAD4 genome ? AF: 0.000203 AC: 23AN: 113094Hom.: 0 Cov.: 24 AF XY: 0.000170 AC XY: 6AN XY: 35236
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Sep 30, 2015 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.868G>T (p.G290W) alteration is located in exon 6 (coding exon 6) of the SYP gene. This alteration results from a G to T substitution at nucleotide position 868, causing the glycine (G) at amino acid position 290 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | SYP: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at