X-100659298-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014467.3(SRPX2):c.164-2878G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0848 in 111,669 control chromosomes in the GnomAD database, including 466 homozygotes. There are 2,960 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_014467.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRPX2 | NM_014467.3 | c.164-2878G>A | intron_variant | ENST00000373004.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRPX2 | ENST00000373004.5 | c.164-2878G>A | intron_variant | 1 | NM_014467.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0847 AC: 9449AN: 111617Hom.: 465 Cov.: 23 AF XY: 0.0872 AC XY: 2948AN XY: 33807
GnomAD4 genome AF: 0.0848 AC: 9469AN: 111669Hom.: 466 Cov.: 23 AF XY: 0.0874 AC XY: 2960AN XY: 33869
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at