10-103602225-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001394015.1(SH3PXD2A):c.2993G>A(p.Arg998Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00014 in 1,597,438 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001394015.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH3PXD2A | NM_001394015.1 | c.2993G>A | p.Arg998Gln | missense_variant | Exon 15 of 15 | ENST00000369774.9 | NP_001380944.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152096Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000157 AC: 37AN: 235434Hom.: 0 AF XY: 0.000158 AC XY: 20AN XY: 126570
GnomAD4 exome AF: 0.000143 AC: 206AN: 1445342Hom.: 0 Cov.: 63 AF XY: 0.000148 AC XY: 106AN XY: 717056
GnomAD4 genome AF: 0.000112 AC: 17AN: 152096Hom.: 0 Cov.: 33 AF XY: 0.0000808 AC XY: 6AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2909G>A (p.R970Q) alteration is located in exon 14 (coding exon 14) of the SH3PXD2A gene. This alteration results from a G to A substitution at nucleotide position 2909, causing the arginine (R) at amino acid position 970 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