rs7833787
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015310.4(PSD3):c.1634+17313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,102 control chromosomes in the GnomAD database, including 15,657 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 0.45 ( 15657 hom., cov: 33)
Consequence
PSD3
NM_015310.4 intron
NM_015310.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.342
Genes affected
PSD3 (HGNC:19093): (pleckstrin and Sec7 domain containing 3) Predicted to enable guanyl-nucleotide exchange factor activity and phospholipid binding activity. Predicted to be involved in regulation of ARF protein signal transduction and regulation of catalytic activity. Predicted to be located in membrane. Predicted to be active in ruffle membrane. [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=-0.98).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSD3 | NM_015310.4 | c.1634+17313T>C | intron_variant | ENST00000327040.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSD3 | ENST00000327040.13 | c.1634+17313T>C | intron_variant | 1 | NM_015310.4 | P3 | |||
PSD3 | ENST00000523619.5 | c.1439+17313T>C | intron_variant | 1 | A2 | ||||
PSD3 | ENST00000519851.5 | c.-44+3737T>C | intron_variant | 5 | |||||
PSD3 | ENST00000518303.5 | n.239+3737T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.446 AC: 67728AN: 151984Hom.: 15644 Cov.: 33
GnomAD3 genomes
?
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67728
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151984
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.446 AC: 67784AN: 152102Hom.: 15657 Cov.: 33 AF XY: 0.448 AC XY: 33339AN XY: 74352
GnomAD4 genome
?
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67784
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152102
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33
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33339
AN XY:
74352
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829
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at