Variant chrX-153592362-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_152274.5(CCNQ):c.657+144C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 601,518 control chromosomes in the GnomAD database, including 856 homozygotes. There are 9,714 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.071 ( 284 hom., 2330 hem., cov: 25)

Exomes 𝑓: 0.051 ( 572 hom. 7384 hem. )

Consequence

CCNQ
NM_152274.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.23

Variant links:

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]

CCNQ links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant X-153592362-G-A is Benign according to our data. Variant chrX-153592362-G-A is described in ClinVar as [Benign]. Clinvar id is 1275895.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CCNQ	NM_152274.5 linkuse as main transcript	c.657+144C>T	intron_variant	ENST00000576892.8
CCNQ	NM_001130997.3 linkuse as main transcript	c.657+144C>T	intron_variant
CCNQ	XM_011531214.3 linkuse as main transcript	c.531+144C>T	intron_variant
CCNQ	XM_047442631.1 linkuse as main transcript	c.429+2185C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCNQ	ENST00000576892.8 linkuse as main transcript	c.657+144C>T		intron_variant		1	NM_152274.5	P1	Q8N1B3-1

Frequencies

GnomAD3 genomes

AF:

0.0712

AC:

8056

AN:

113111

Hom.:

284

Cov.:

AF XY:

0.0660

AC XY:

2325

AN XY:

35247

show subpopulations

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.0117

Gnomad AMR

AF:

0.0370

Gnomad ASJ

AF:

0.0113

Gnomad EAS

AF:

0.0299

Gnomad SAS

AF:

0.0495

Gnomad FIN

AF:

0.0302

Gnomad MID

AF:

0.0336

Gnomad NFE

AF:

0.0493

Gnomad OTH

AF:

0.0804

GnomAD4 exome

AF:

0.0513

AC:

25070

AN:

488353

Hom.:

572

AF XY:

0.0527

AC XY:

7384

AN XY:

140105

show subpopulations

Gnomad4 AFR exome

AF:

0.153

Gnomad4 AMR exome

AF:

0.0288

Gnomad4 ASJ exome

AF:

0.00948

Gnomad4 EAS exome

AF:

0.0329

Gnomad4 SAS exome

AF:

0.0541

Gnomad4 FIN exome

AF:

0.0288

Gnomad4 NFE exome

AF:

0.0529

Gnomad4 OTH exome

AF:

0.0517

GnomAD4 genome

AF:

0.0712

AC:

8061

AN:

113165

Hom.:

284

Cov.:

AF XY:

0.0660

AC XY:

2330

AN XY:

35311

show subpopulations

Gnomad4 AFR

AF:

0.142

Gnomad4 AMR

AF:

0.0369

Gnomad4 ASJ

AF:

0.0113

Gnomad4 EAS

AF:

0.0297

Gnomad4 SAS

AF:

0.0485

Gnomad4 FIN

AF:

0.0302

Gnomad4 NFE

AF:

0.0493

Gnomad4 OTH

AF:

0.0794

Alfa

AF:

0.0485

Hom.:

2683

Bravo

AF:

0.0750

ClinVar

Significance: 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	GeneDx	Nov 11, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.082

DANN

Benign

0.70

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over