X-100644247-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014467.3(SRPX2):c.-399G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 111,205 control chromosomes in the GnomAD database, including 940 homozygotes. There are 4,528 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.14 ( 940 hom., 4525 hem., cov: 22)
Exomes 𝑓: 0.16 ( 0 hom. 3 hem. )
Consequence
SRPX2
NM_014467.3 5_prime_UTR
NM_014467.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.444
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=-0.79).
BP6
?
Variant X-100644247-G-C is Benign according to our data. Variant chrX-100644247-G-C is described in ClinVar as [Benign]. Clinvar id is 1260803.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRPX2 | NM_014467.3 | c.-399G>C | 5_prime_UTR_variant | 1/11 | ENST00000373004.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRPX2 | ENST00000373004.5 | c.-399G>C | 5_prime_UTR_variant | 1/11 | 1 | NM_014467.3 | P1 | ||
SRPX2 | ENST00000640889.1 | c.-270G>C | 5_prime_UTR_variant | 1/7 | 5 | ||||
SRPX2 | ENST00000481988.1 | n.27G>C | non_coding_transcript_exon_variant | 1/3 | 3 | ||||
SRPX2 | ENST00000640020.1 | n.49G>C | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.143 AC: 15898AN: 111127Hom.: 939 Cov.: 22 AF XY: 0.135 AC XY: 4497AN XY: 33379
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GnomAD4 exome AF: 0.160 AC: 4AN: 25Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 3AN XY: 15
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GnomAD4 genome ? AF: 0.143 AC: 15928AN: 111180Hom.: 940 Cov.: 22 AF XY: 0.135 AC XY: 4525AN XY: 33442
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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 | Jun 10, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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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