Variant chrX-49246636-A-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_014008.5(CCDC22):c.715-95A>T 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 0.61 ( 15176 hom., 19838 hem., cov: 23)

Exomes 𝑓: 0.70 ( 122015 hom. 121619 hem. )

Failed GnomAD Quality Control

Consequence

CCDC22
NM_014008.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.186

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 Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CCDC22	NM_014008.5 linkuse as main transcript	c.715-95A>T	intron_variant	ENST00000376227.4
CCDC22	XM_005272599.5 linkuse as main transcript	c.712-95A>T	intron_variant
CCDC22	XR_430506.4 linkuse as main transcript	n.882-95A>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC22	ENST00000376227.4 linkuse as main transcript	c.715-95A>T		intron_variant		1	NM_014008.5	P1

Frequencies

GnomAD3 genomes

AF:

0.605

AC:

67188

AN:

110963

Hom.:

15177

Cov.:

AF XY:

0.596

AC XY:

19799

AN XY:

33215

show subpopulations

Gnomad AFR

AF:

0.434

Gnomad AMI

AF:

0.636

Gnomad AMR

AF:

0.531

Gnomad ASJ

AF:

0.771

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.668

Gnomad FIN

AF:

0.635

Gnomad MID

AF:

0.713

Gnomad NFE

AF:

0.718

Gnomad OTH

AF:

0.614

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.705

AC:

463812

AN:

657948

Hom.:

122015

AF XY:

0.715

AC XY:

121619

AN XY:

170214

show subpopulations

Gnomad4 AFR exome

AF:

0.442

Gnomad4 AMR exome

AF:

0.509

Gnomad4 ASJ exome

AF:

0.762

Gnomad4 EAS exome

AF:

0.399

Gnomad4 SAS exome

AF:

0.697

Gnomad4 FIN exome

AF:

0.649

Gnomad4 NFE exome

AF:

0.737

Gnomad4 OTH exome

AF:

0.676

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.605

AC:

67216

AN:

111016

Hom.:

15176

Cov.:

AF XY:

0.596

AC XY:

19838

AN XY:

33278

show subpopulations

Gnomad4 AFR

AF:

0.434

Gnomad4 AMR

AF:

0.531

Gnomad4 ASJ

AF:

0.771

Gnomad4 EAS

AF:

0.385

Gnomad4 SAS

AF:

0.670

Gnomad4 FIN

AF:

0.635

Gnomad4 NFE

AF:

0.718

Gnomad4 OTH

AF:

0.615

Alfa

AF:

0.649

Hom.:

5087

Bravo

AF:

0.586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.19

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over