rs12010175

Positions:

• chrX-153597180-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_152274.5(CCNQ):​c.113-993T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.89 (31001 hom., 28928 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: CCNQ NM_152274.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCNQ	NM_152274.5	c.113-993T>C		intron_variant		ENST00000576892.8	NP_689487.2
CCNQ	NM_001130997.3	c.113-993T>C		intron_variant			NP_001124469.1
CCNQ	XM_011531214.3	c.-15+242T>C		intron_variant			XP_011529516.1
CCNQ	XM_047442631.1	c.113-993T>C		intron_variant			XP_047298587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNQ	ENST00000576892.8	c.113-993T>C		intron_variant		1	NM_152274.5	ENSP00000461135.1

Frequencies

GnomAD3 genomes AF: 0.889 AC: 98152 AN: 110376 Hom.: 31005 Cov.: 23 AF XY: 0.887 AC XY: 28885 AN XY: 32572

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.926

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.958

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.910

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.889 AC: 98187 AN: 110428 Hom.: 31001 Cov.: 23 AF XY: 0.886 AC XY: 28928 AN XY: 32634

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.911

Alfa AF: 0.927 Hom.: 58970

Bravo AF: 0.879

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	9.7
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12010175; hg19: chrX-152862638;