X-49242913-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_014008.5(CCDC22):c.389T>C(p.Ile130Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00145 in 1,163,848 control chromosomes in the GnomAD database, including 3 homozygotes. There are 503 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0021 ( 0 hom., 104 hem., cov: 23)
Exomes 𝑓: 0.0014 ( 3 hom. 399 hem. )
Consequence
CCDC22
NM_014008.5 missense
NM_014008.5 missense
Scores
11
5
Clinical Significance
Conservation
PhyloP100: 6.05
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0091558695).
BP6
?
Variant X-49242913-T-C is Benign according to our data. Variant chrX-49242913-T-C is described in ClinVar as [Benign]. Clinvar id is 713437.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-49242913-T-C is described in Lovd as [Benign].
BS2
?
High Hemizygotes in GnomAd at 104 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC22 | NM_014008.5 | c.389T>C | p.Ile130Thr | missense_variant | 4/17 | ENST00000376227.4 | |
CCDC22 | XM_005272599.5 | c.389T>C | p.Ile130Thr | missense_variant | 4/17 | ||
CCDC22 | XR_430506.4 | n.556T>C | non_coding_transcript_exon_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC22 | ENST00000376227.4 | c.389T>C | p.Ile130Thr | missense_variant | 4/17 | 1 | NM_014008.5 | P1 | |
CCDC22 | ENST00000490300.1 | n.532T>C | non_coding_transcript_exon_variant | 3/5 | 3 | ||||
CCDC22 | ENST00000496651.5 | n.480T>C | non_coding_transcript_exon_variant | 4/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00205 AC: 229AN: 111527Hom.: 0 Cov.: 23 AF XY: 0.00308 AC XY: 104AN XY: 33719
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GnomAD3 exomes AF: 0.00275 AC: 351AN: 127551Hom.: 0 AF XY: 0.00227 AC XY: 67AN XY: 29451
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GnomAD4 exome AF: 0.00139 AC: 1463AN: 1052268Hom.: 3 Cov.: 29 AF XY: 0.00119 AC XY: 399AN XY: 334436
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Benign
Dann
Uncertain
DEOGEN2
Uncertain
D
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at