rs923799
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394015.1(SH3PXD2A):c.399-15081T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,008 control chromosomes in the GnomAD database, including 18,717 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.49 ( 18717 hom., cov: 32)
Consequence
SH3PXD2A
NM_001394015.1 intron
NM_001394015.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.108
Genes affected
SH3PXD2A (HGNC:23664): (SH3 and PX domains 2A) Predicted to enable superoxide-generating NADPH oxidase activator activity. Involved in osteoclast fusion and superoxide metabolic process. Located in podosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3PXD2A | NM_001394015.1 | c.399-15081T>C | intron_variant | ENST00000369774.9 | |||
SH3PXD2A | NM_014631.3 | c.399-15081T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3PXD2A | ENST00000369774.9 | c.399-15081T>C | intron_variant | 5 | NM_001394015.1 | P4 | |||
SH3PXD2A | ENST00000355946.7 | c.399-15081T>C | intron_variant | 1 | A1 | ||||
SH3PXD2A | ENST00000687380.1 | c.399-15081T>C | intron_variant | ||||||
SH3PXD2A | ENST00000692756.1 | n.256-15081T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.489 AC: 74321AN: 151890Hom.: 18697 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.489 AC: 74389AN: 152008Hom.: 18717 Cov.: 32 AF XY: 0.490 AC XY: 36422AN XY: 74312
GnomAD4 genome
?
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32
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36422
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1695
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at