4-2818279-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001145856.2(SH3BP2):c.56G>A(p.Arg19Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 146,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145856.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH3BP2 | NM_001122681.2 | c.-4-2335G>A | intron_variant | ENST00000503393.8 | NP_001116153.1 | |||
SH3BP2 | NM_001145856.2 | c.56G>A | p.Arg19Gln | missense_variant | 1/13 | NP_001139328.1 | ||
SH3BP2 | NM_001145855.2 | c.81-2335G>A | intron_variant | NP_001139327.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000136 AC: 2AN: 146952Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 29
GnomAD4 genome AF: 0.0000136 AC: 2AN: 146952Hom.: 0 Cov.: 32 AF XY: 0.0000280 AC XY: 2AN XY: 71466
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2024 | The c.56G>A (p.R19Q) alteration is located in exon 1 (coding exon 1) of the SH3BP2 gene. This alteration results from a G to A substitution at nucleotide position 56, causing the arginine (R) at amino acid position 19 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at