Variant chrX-49249149-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_014008.5(CCDC22):c.1540-18T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 10557 hom., 16860 hem., cov: 24)

Exomes 𝑓: 0.57 ( 120278 hom. 201744 hem. )

Failed GnomAD Quality Control

Consequence

CCDC22
NM_014008.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.97

Variant links:

Genes affected

CCDC22 (HGNC:28909): (coiled-coil domain containing 22) This gene encodes a protein containing a coiled-coil domain. The encoded protein functions in the regulation of NF-kB (nuclear factor kappa-light-chain-enhancer of activated B cells) by interacting with COMMD (copper metabolism Murr1 domain-containing) proteins. The mouse orthologous protein has been shown to bind copines, which are calcium-dependent, membrane-binding proteins that may function in calcium signaling. This human gene has been identified as a novel candidate gene for syndromic X-linked intellectual disability. [provided by RefSeq, Aug 2013]

CCDC22 links:

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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=-0.84).

BP6

Variant X-49249149-T-C is Benign according to our data. Variant chrX-49249149-T-C is described in ClinVar as [Benign]. Clinvar id is 284920.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC22	NM_014008.5 linkuse as main transcript	c.1540-18T>C		intron_variant		ENST00000376227.4	NP_054727.1	O60826A0A024QZ03
CCDC22	XM_005272599.5 linkuse as main transcript	c.1537-18T>C		intron_variant			XP_005272656.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC22	ENST00000376227.4 linkuse as main transcript	c.1540-18T>C		intron_variant		1	NM_014008.5	ENSP00000365401.3		O60826

Frequencies

GnomAD3 genomes

AF:

0.508

AC:

56780

AN:

111703

Hom.:

10555

Cov.:

AF XY:

0.496

AC XY:

16820

AN XY:

33919

show subpopulations

Gnomad AFR

AF:

0.408

Gnomad AMI

AF:

0.520

Gnomad AMR

AF:

0.441

Gnomad ASJ

AF:

0.581

Gnomad EAS

AF:

0.383

Gnomad SAS

AF:

0.572

Gnomad FIN

AF:

0.491

Gnomad MID

AF:

0.580

Gnomad NFE

AF:

0.583

Gnomad OTH

AF:

0.506

GnomAD3 exomes

AF:

0.522

AC:

91508

AN:

175177

Hom.:

15626

AF XY:

0.535

AC XY:

32675

AN XY:

61021

show subpopulations

Gnomad AFR exome

AF:

0.411

Gnomad AMR exome

AF:

0.407

Gnomad ASJ exome

AF:

0.578

Gnomad EAS exome

AF:

0.391

Gnomad SAS exome

AF:

0.585

Gnomad FIN exome

AF:

0.513

Gnomad NFE exome

AF:

0.585

Gnomad OTH exome

AF:

0.532

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.572

AC:

618923

AN:

1082239

Hom.:

120278

Cov.:

AF XY:

0.577

AC XY:

201744

AN XY:

349721

show subpopulations

Gnomad4 AFR exome

AF:

0.407

Gnomad4 AMR exome

AF:

0.413

Gnomad4 ASJ exome

AF:

0.585

Gnomad4 EAS exome

AF:

0.396

Gnomad4 SAS exome

AF:

0.581

Gnomad4 FIN exome

AF:

0.510

Gnomad4 NFE exome

AF:

0.593

Gnomad4 OTH exome

AF:

0.556

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.508

AC:

56814

AN:

111755

Hom.:

10557

Cov.:

AF XY:

0.496

AC XY:

16860

AN XY:

33981

show subpopulations

Gnomad4 AFR

AF:

0.408

Gnomad4 AMR

AF:

0.441

Gnomad4 ASJ

AF:

0.581

Gnomad4 EAS

AF:

0.384

Gnomad4 SAS

AF:

0.574

Gnomad4 FIN

AF:

0.491

Gnomad4 NFE

AF:

0.583

Gnomad4 OTH

AF:

0.510

Alfa

AF:

0.565

Hom.:

41044

Bravo

AF:

0.498

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Dec 07, 2015

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Ritscher-Schinzel syndrome 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.26

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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