rs150552508
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4BP6_Very_StrongBP7BS2
The NM_014467.3(SRPX2):c.481C>A(p.Arg161Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00174 in 1,209,407 control chromosomes in the GnomAD database, including 3 homozygotes. There are 635 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_014467.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000989 AC: 111AN: 112178Hom.: 0 Cov.: 23 AF XY: 0.000669 AC XY: 23AN XY: 34368
GnomAD3 exomes AF: 0.00102 AC: 184AN: 179696Hom.: 0 AF XY: 0.00111 AC XY: 72AN XY: 64690
GnomAD4 exome AF: 0.00181 AC: 1989AN: 1097174Hom.: 3 Cov.: 32 AF XY: 0.00169 AC XY: 612AN XY: 362670
GnomAD4 genome AF: 0.000989 AC: 111AN: 112233Hom.: 0 Cov.: 23 AF XY: 0.000668 AC XY: 23AN XY: 34433
ClinVar
Submissions by phenotype
not specified Benign:4
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This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Benign:2
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Rolandic epilepsy, intellectual disability, and speech dyspraxia, X-linked Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at