rs139339184
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_006662.3(SRCAP):c.1559G>A(p.Ser520Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000889 in 1,613,902 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006662.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRCAP | NM_006662.3 | c.1559G>A | p.Ser520Asn | missense_variant | 12/34 | ENST00000262518.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRCAP | ENST00000262518.9 | c.1559G>A | p.Ser520Asn | missense_variant | 12/34 | 2 | NM_006662.3 | P1 | |
SRCAP | ENST00000411466.7 | c.1559G>A | p.Ser520Asn | missense_variant | 12/34 | 3 | P1 | ||
SRCAP | ENST00000706321.1 | c.1559G>A | p.Ser520Asn | missense_variant | 12/34 | P1 | |||
SRCAP | ENST00000483083.3 | c.659G>A | p.Ser220Asn | missense_variant | 5/18 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000941 AC: 143AN: 152018Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00125 AC: 314AN: 251278Hom.: 3 AF XY: 0.00135 AC XY: 183AN XY: 135802
GnomAD4 exome AF: 0.000884 AC: 1292AN: 1461766Hom.: 7 Cov.: 32 AF XY: 0.000930 AC XY: 676AN XY: 727164
GnomAD4 genome ? AF: 0.000940 AC: 143AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.000955 AC XY: 71AN XY: 74380
ClinVar
Submissions by phenotype
not provided Benign:6
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 10, 2017 | - - |
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | SRCAP: BS1, BS2 - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 01, 2024 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Jul 17, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 15, 2018 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 10, 2022 | This alteration is classified as 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at