rs572213217
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_018451.5(CENPJ):āc.810A>Gā(p.Gln270=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000545 in 1,614,026 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00032 ( 1 hom., cov: 32)
Exomes š: 0.00057 ( 13 hom. )
Consequence
CENPJ
NM_018451.5 synonymous
NM_018451.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.484
Genes affected
CENPJ (HGNC:17272): (centromere protein J) This gene encodes a protein that belongs to the centromere protein family. During cell division, this protein plays a structural role in the maintenance of centrosome integrity and normal spindle morphology, and it is involved in microtubule disassembly at the centrosome. This protein can function as a transcriptional coactivator in the Stat5 signaling pathway, and also as a coactivator of NF-kappaB-mediated transcription, likely via its interaction with the coactivator p300/CREB-binding protein. Mutations in this gene are associated with primary autosomal recessive microcephaly, a disorder characterized by severely reduced brain size and cognitive disability. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 13-24909845-T-C is Benign according to our data. Variant chr13-24909845-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 158221.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.484 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000322 (49/152360) while in subpopulation SAS AF= 0.0102 (49/4826). AF 95% confidence interval is 0.00789. There are 1 homozygotes in gnomad4. There are 37 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPJ | NM_018451.5 | c.810A>G | p.Gln270= | synonymous_variant | 4/17 | ENST00000381884.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPJ | ENST00000381884.9 | c.810A>G | p.Gln270= | synonymous_variant | 4/17 | 1 | NM_018451.5 | P1 | |
CENPJ | ENST00000616936.4 | c.810A>G | p.Gln270= | synonymous_variant, NMD_transcript_variant | 4/16 | 1 | |||
CENPJ | ENST00000545981.6 | c.810A>G | p.Gln270= | synonymous_variant, NMD_transcript_variant | 4/18 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000309 AC: 47AN: 152242Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00116 AC: 292AN: 251064Hom.: 2 AF XY: 0.00160 AC XY: 217AN XY: 135736
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GnomAD4 exome AF: 0.000568 AC: 830AN: 1461666Hom.: 13 Cov.: 31 AF XY: 0.000824 AC XY: 599AN XY: 727130
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GnomAD4 genome ? AF: 0.000322 AC: 49AN: 152360Hom.: 1 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74506
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 12, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
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Name
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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