10-103601838-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_001394015.1(SH3PXD2A):c.3380A>C(p.Asn1127Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000373 in 1,607,744 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH3PXD2A | NM_001394015.1 | c.3380A>C | p.Asn1127Thr | missense_variant | Exon 15 of 15 | ENST00000369774.9 | NP_001380944.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151632Hom.: 0 Cov.: 29
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1456112Hom.: 0 Cov.: 32 AF XY: 0.00000414 AC XY: 3AN XY: 724124
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151632Hom.: 0 Cov.: 29 AF XY: 0.0000135 AC XY: 1AN XY: 74022
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3296A>C (p.N1099T) alteration is located in exon 14 (coding exon 14) of the SH3PXD2A gene. This alteration results from a A to C substitution at nucleotide position 3296, causing the asparagine (N) at amino acid position 1099 to be replaced by a threonine (T). 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