rs556230791
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_ModerateBP6_Very_StrongBS2
The NM_006662.3(SRCAP):c.3292C>T(p.Arg1098Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,613,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1098P) has been classified as Likely benign.
Frequency
Consequence
NM_006662.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRCAP | NM_006662.3 | c.3292C>T | p.Arg1098Trp | missense_variant | 21/34 | ENST00000262518.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRCAP | ENST00000262518.9 | c.3292C>T | p.Arg1098Trp | missense_variant | 21/34 | 2 | NM_006662.3 | P1 | |
SRCAP | ENST00000411466.7 | c.3292C>T | p.Arg1098Trp | missense_variant | 21/34 | 3 | P1 | ||
SRCAP | ENST00000706321.1 | c.3292C>T | p.Arg1098Trp | missense_variant | 21/34 | P1 | |||
SRCAP | ENST00000483083.3 | c.2392C>T | p.Arg798Trp | missense_variant | 14/18 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248296Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134266
GnomAD4 exome AF: 0.0000671 AC: 98AN: 1460998Hom.: 0 Cov.: 33 AF XY: 0.0000729 AC XY: 53AN XY: 726774
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital | Jul 17, 2017 | BS1, BS2, BP1; This alteration has an allele frequency that is greater than expected for the associated disease, was seen in a healthy adult where full penetrance of the disorder is expected at an early age, and is a missense alteration in a gene for which primarily truncating variants are known to cause disease. - |
Floating-Harbor syndrome;C5562012:Developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 28, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at