chr4-2818442-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001122681.2(SH3BP2):c.-4-2172C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0988 in 1,006,900 control chromosomes in the GnomAD database, including 5,115 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.10 ( 855 hom., cov: 33)
Exomes 𝑓: 0.098 ( 4260 hom. )
Consequence
SH3BP2
NM_001122681.2 intron
NM_001122681.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.83
Genes affected
SH3BP2 (HGNC:10825): (SH3 domain binding protein 2) The protein encoded by this gene has an N-terminal pleckstrin homology (PH) domain, an SH3-binding proline-rich region, and a C-terminal SH2 domain. The protein binds to the SH3 domains of several proteins including the ABL1 and SYK protein tyrosine kinases , and functions as a cytoplasmic adaptor protein to positively regulate transcriptional activity in T, natural killer (NK), and basophilic cells. Mutations in this gene result in cherubism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
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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=-0.85).
BP6
?
Variant 4-2818442-C-G is Benign according to our data. Variant chr4-2818442-C-G is described in ClinVar as [Benign]. Clinvar id is 1226123.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3BP2 | NM_001122681.2 | c.-4-2172C>G | intron_variant | ENST00000503393.8 | |||
SH3BP2 | NM_001145855.2 | c.81-2172C>G | intron_variant | ||||
SH3BP2 | NM_001145856.2 | c.167+52C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3BP2 | ENST00000503393.8 | c.-4-2172C>G | intron_variant | 1 | NM_001122681.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.101 AC: 15351AN: 151474Hom.: 855 Cov.: 33
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GnomAD4 exome AF: 0.0984 AC: 84147AN: 855320Hom.: 4260 AF XY: 0.0990 AC XY: 40076AN XY: 404970
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GnomAD4 genome ? AF: 0.101 AC: 15352AN: 151580Hom.: 855 Cov.: 33 AF XY: 0.103 AC XY: 7662AN XY: 74086
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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 | May 16, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at