rs766670891
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_014467.3(SRPX2):c.99G>A(p.Pro33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000993 in 1,208,591 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P33P) has been classified as Likely benign.
Frequency
Consequence
NM_014467.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRPX2 | NM_014467.3 | c.99G>A | p.Pro33= | synonymous_variant | 3/11 | ENST00000373004.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRPX2 | ENST00000373004.5 | c.99G>A | p.Pro33= | synonymous_variant | 3/11 | 1 | NM_014467.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000269 AC: 3AN: 111549Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33737
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183209Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67663
GnomAD4 exome AF: 0.00000820 AC: 9AN: 1097042Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 1AN XY: 362420
GnomAD4 genome ? AF: 0.0000269 AC: 3AN: 111549Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33737
ClinVar
Submissions by phenotype
Rolandic epilepsy, intellectual disability, and speech dyspraxia, X-linked Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 06, 2021 | Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with SRPX2-related conditions. This variant is present in population databases (rs766670891, ExAC 0.01%). This sequence change affects codon 33 of the SRPX2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the SRPX2 protein. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at