rs6609857

chrX-49245158-T-CchrX-49245158-T-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_014008.5(CCDC22):c.715-1573T>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 0.61 (15470 hom., 17085 hem., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: CCDC22 NM_014008.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS2: High Homozygotes in GnomAd at 15471 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC22	NM_014008.5	c.715-1573T>C		intron_variant		ENST00000376227.4
CCDC22	XM_005272599.5	c.712-1573T>C		intron_variant
CCDC22	XR_430506.4	n.882-1573T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC22	ENST00000376227.4	c.715-1573T>C		intron_variant		1	NM_014008.5	P1

Frequencies

GnomAD3 genomes AF: 0.611 AC: 64946 AN: 106265 Hom.: 15471 Cov.: 19 AF XY: 0.590 AC XY: 17049 AN XY: 28911

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.625

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: 0.611 AC: 64972 AN: 106324 Hom.: 15470 Cov.: 19 AF XY: 0.590 AC XY: 17085 AN XY: 28978

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.626

Alfa AF: 0.656 Hom.: 6553

Bravo AF: 0.597

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6609857; hg19: chrX-49101623;