X-100650801-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014467.3(SRPX2):c.99G>T(p.Pro33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000182 in 1,097,044 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P33P) has been classified as Uncertain significance.
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>T | 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>T | p.Pro33= | synonymous_variant | 3/11 | 1 | NM_014467.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183209Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67663
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097044Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 1AN XY: 362422
GnomAD4 genome ? Cov.: 22
ClinVar
Submissions by phenotype
Rolandic epilepsy, intellectual disability, and speech dyspraxia, X-linked Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 06, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at