rs6794128
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015009.3(PDZRN3):c.918+88371C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,060 control chromosomes in the GnomAD database, including 19,497 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 0.50 ( 19497 hom., cov: 33)
Consequence
PDZRN3
NM_015009.3 intron
NM_015009.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.28
Genes affected
PDZRN3 (HGNC:17704): (PDZ domain containing ring finger 3) This gene encodes a member of the LNX (Ligand of Numb Protein-X) family of RING-type ubiquitin E3 ligases. This protein may function in vascular morphogenesis and the differentiation of adipocytes, osteoblasts and myoblasts. This protein may be targeted for degradation by the human papilloma virus E6 protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
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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=-0.73).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDZRN3 | NM_015009.3 | c.918+88371C>T | intron_variant | ENST00000263666.9 | NP_055824.1 | |||
PDZRN3 | NM_001303139.2 | c.12+55168C>T | intron_variant | NP_001290068.1 | ||||
PDZRN3 | NM_001303140.2 | c.-112+47468C>T | intron_variant | NP_001290069.1 | ||||
PDZRN3 | XM_017005942.3 | c.831+88371C>T | intron_variant | XP_016861431.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDZRN3 | ENST00000263666.9 | c.918+88371C>T | intron_variant | 1 | NM_015009.3 | ENSP00000263666.4 |
Frequencies
GnomAD3 genomes AF: 0.503 AC: 76467AN: 151942Hom.: 19478 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.503 AC: 76522AN: 152060Hom.: 19497 Cov.: 33 AF XY: 0.508 AC XY: 37765AN XY: 74320
GnomAD4 genome
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1743
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3476
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