rs6609857

Variant names:

• chrX-49245158-T-C
• rs6609857
• NM_014008.5:c.715-1573T>C

Your query was ambiguous. Multiple possible variants found:

• chrX-49245158-T-C
• chrX-49245158-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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
• Publications: 8 publications found

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 Gene-Disease associations (from GenCC):

• Ritscher-Schinzel syndrome 2

  Inheritance: XL Classification: STRONG, MODERATE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen
• Ritscher-Schinzel syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• epilepsy

  Inheritance: XL Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014008.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC22	NM_014008.5	MANE Select	c.715-1573T>C		intron	N/A	NP_054727.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC22	ENST00000376227.4	TSL:1 MANE Select	c.715-1573T>C		intron	N/A	ENSP00000365401.3
	CCDC22	ENST00000960401.1		c.739-1573T>C		intron	N/A	ENSP00000630460.1
	CCDC22	ENST00000904959.1		c.733-1573T>C		intron	N/A	ENSP00000575018.1

Frequencies

GnomAD3 genomes AF: 0.611 AC: 64946 AN: 106265 Hom.: 15471 Cov.: 19

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

African (AFR) AF: 0.455 AC: 13260 AN: 29121

American (AMR) AF: 0.532 AC: 5312 AN: 9989

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2078 AN: 2577

East Asian (EAS) AF: 0.374 AC: 1237 AN: 3311

South Asian (SAS) AF: 0.662 AC: 1522 AN: 2298

European-Finnish (FIN) AF: 0.610 AC: 3257 AN: 5341

Middle Eastern (MID) AF: 0.701 AC: 143 AN: 204

European-Non Finnish (NFE) AF: 0.717 AC: 36852 AN: 51392

Other (OTH) AF: 0.626 AC: 908 AN: 1450

Alfa AF: 0.656 Hom.: 6553

Bravo AF: 0.597

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs6609857; hg19: chrX-49101623;