rs11681930
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001302769.2(PARD3B):c.2140+5254G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,014 control chromosomes in the GnomAD database, including 5,017 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 0.25 ( 5017 hom., cov: 32)
Consequence
PARD3B
NM_001302769.2 intron
NM_001302769.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0760
Genes affected
PARD3B (HGNC:14446): (par-3 family cell polarity regulator beta) Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in several processes, including establishment of cell polarity; establishment of centrosome localization; and establishment or maintenance of epithelial cell apical/basal polarity. Located in cell junction. Part of protein-containing complex. [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=-0.86).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARD3B | NM_001302769.2 | c.2140+5254G>A | intron_variant | ENST00000406610.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARD3B | ENST00000406610.7 | c.2140+5254G>A | intron_variant | 1 | NM_001302769.2 | P1 | |||
PARD3B | ENST00000349953.7 | c.2140+5254G>A | intron_variant | 1 | |||||
PARD3B | ENST00000351153.5 | c.2140+5254G>A | intron_variant | 1 | |||||
PARD3B | ENST00000358768.6 | c.1954+5254G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.247 AC: 37538AN: 151896Hom.: 5003 Cov.: 32
GnomAD3 genomes
?
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37538
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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: 0.247 AC: 37585AN: 152014Hom.: 5017 Cov.: 32 AF XY: 0.246 AC XY: 18268AN XY: 74278
GnomAD4 genome
?
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37585
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152014
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32
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18268
AN XY:
74278
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825
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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