rs376050298
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_152274.5(CCNQ):c.669C>T(p.Asp223=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 1,199,793 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 110 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., 6 hem., cov: 24)
Exomes 𝑓: 0.00027 ( 0 hom. 104 hem. )
Consequence
CCNQ
NM_152274.5 synonymous
NM_152274.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.536
Genes affected
CCNQ (HGNC:28434): (cyclin Q) Mutations in this gene have been shown to cause an X-linked dominant STAR syndrome that typically manifests syndactyly, telecanthus and anogenital and renal malformations. The protein encoded by this gene contains a cyclin-box-fold domain which suggests it may have a role in controlling nuclear cell division cycles. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant X-153588443-G-A is Benign according to our data. Variant chrX-153588443-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 445928.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.536 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd4 at 6 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCNQ | NM_152274.5 | c.669C>T | p.Asp223= | synonymous_variant | 5/5 | ENST00000576892.8 | |
CCNQ | XM_011531214.3 | c.543C>T | p.Asp181= | synonymous_variant | 5/5 | ||
CCNQ | XM_047442631.1 | c.441C>T | p.Asp147= | synonymous_variant | 4/4 | ||
CCNQ | NM_001130997.3 | c.658-49C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCNQ | ENST00000576892.8 | c.669C>T | p.Asp223= | synonymous_variant | 5/5 | 1 | NM_152274.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000115 AC: 13AN: 112596Hom.: 0 Cov.: 24 AF XY: 0.000173 AC XY: 6AN XY: 34734
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GnomAD3 exomes AF: 0.000158 AC: 29AN: 183102Hom.: 0 AF XY: 0.000207 AC XY: 14AN XY: 67616
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GnomAD4 exome AF: 0.000273 AC: 297AN: 1087144Hom.: 0 Cov.: 28 AF XY: 0.000295 AC XY: 104AN XY: 353034
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GnomAD4 genome ? AF: 0.000115 AC: 13AN: 112649Hom.: 0 Cov.: 24 AF XY: 0.000172 AC XY: 6AN XY: 34797
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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 provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 27, 2017 | - - |
Computational scores
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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