chrX-49191497-G-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_003179.3(SYP):c.882C>G(p.Asp294Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000826 in 1,210,379 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003179.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYP | NM_003179.3 | c.882C>G | p.Asp294Glu | missense_variant | 6/7 | ENST00000263233.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYP | ENST00000263233.9 | c.882C>G | p.Asp294Glu | missense_variant | 6/7 | 1 | NM_003179.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000707 AC: 8AN: 113101Hom.: 0 Cov.: 24 AF XY: 0.0000851 AC XY: 3AN XY: 35235
GnomAD3 exomes AF: 0.0000113 AC: 2AN: 177687Hom.: 0 AF XY: 0.0000154 AC XY: 1AN XY: 64819
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097278Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 1AN XY: 362944
GnomAD4 genome ? AF: 0.0000707 AC: 8AN: 113101Hom.: 0 Cov.: 24 AF XY: 0.0000851 AC XY: 3AN XY: 35235
ClinVar
Submissions by phenotype
Intellectual disability, X-linked 96 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at