X-100651156-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014467.3(SRPX2):c.163+291T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0381 in 326,104 control chromosomes in the GnomAD database, including 414 homozygotes. There are 3,924 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.048 ( 202 hom., 1671 hem., cov: 22)
Exomes 𝑓: 0.033 ( 212 hom. 2253 hem. )
Consequence
SRPX2
NM_014467.3 intron
NM_014467.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.551
Genes affected
SRPX2 (HGNC:30668): (sushi repeat containing protein X-linked 2) This gene encodes a secreted protein that contains three sushi repeat motifs. The encoded protein may play a role in the development of speech and language centers in the brain. This protein may also be involved in angiogenesis. Mutations in this gene are the cause of bilateral perisylvian polymicrogyria, rolandic epilepsy, speech dyspraxia and cognitive disability. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant X-100651156-T-G is Benign according to our data. Variant chrX-100651156-T-G is described in ClinVar as [Benign]. Clinvar id is 1247373.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRPX2 | NM_014467.3 | c.163+291T>G | intron_variant | ENST00000373004.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRPX2 | ENST00000373004.5 | c.163+291T>G | intron_variant | 1 | NM_014467.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0484 AC: 5379AN: 111235Hom.: 201 Cov.: 22 AF XY: 0.0497 AC XY: 1663AN XY: 33455
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GnomAD4 exome AF: 0.0327 AC: 7033AN: 214814Hom.: 212 AF XY: 0.0435 AC XY: 2253AN XY: 51794
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GnomAD4 genome ? AF: 0.0485 AC: 5394AN: 111290Hom.: 202 Cov.: 22 AF XY: 0.0499 AC XY: 1671AN XY: 33520
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at