rs1966983
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178140.4(PDZD2):c.-360-53117C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 149,772 control chromosomes in the GnomAD database, including 6,834 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 0.29 ( 6834 hom., cov: 31)
Consequence
PDZD2
NM_178140.4 intron
NM_178140.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.470
Genes affected
PDZD2 (HGNC:18486): (PDZ domain containing 2) The protein encoded by this gene contains six PDZ domains and shares sequence similarity with pro-interleukin-16 (pro-IL-16). Like pro-IL-16, the encoded protein localizes to the endoplasmic reticulum and is thought to be cleaved by a caspase to produce a secreted peptide containing two PDZ domains. In addition, this gene is upregulated in primary prostate tumors and may be involved in the early stages of prostate tumorigenesis. [provided by RefSeq, Dec 2015]
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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=-0.93).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD2 | NM_178140.4 | c.-360-53117C>A | intron_variant | ENST00000438447.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD2 | ENST00000438447.2 | c.-360-53117C>A | intron_variant | 1 | NM_178140.4 | P1 | |||
PDZD2 | ENST00000502824.1 | n.88+52798C>A | intron_variant, non_coding_transcript_variant | 1 | |||||
PDZD2 | ENST00000513910.1 | c.-443+33681C>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.295 AC: 44147AN: 149688Hom.: 6829 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.295 AC: 44167AN: 149772Hom.: 6834 Cov.: 31 AF XY: 0.298 AC XY: 21708AN XY: 72942
GnomAD4 genome
?
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44167
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31
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21708
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72942
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1477
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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