8-93726443-T-G
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_145269.5(CIBAR1):āc.707T>Gā(p.Ile236Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000296 in 1,613,716 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: š 0.0017 ( 0 hom., cov: 32)
Exomes š: 0.00015 ( 0 hom. )
Consequence
CIBAR1
NM_145269.5 missense
NM_145269.5 missense
Scores
2
8
8
Clinical Significance
Conservation
PhyloP100: 4.51
Genes affected
CIBAR1 (HGNC:30452): (CBY1 interacting BAR domain containing 1) Enables phospholipid binding activity. Involved in several processes, including inner mitochondrial membrane organization; limb morphogenesis; and membrane tubulation. Located in several cellular components, including centriole; ciliary base; and mitochondrial crista. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.010921121).
BP6
Variant 8-93726443-T-G is Benign according to our data. Variant chr8-93726443-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 3036032.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CIBAR1 | NM_145269.5 | c.707T>G | p.Ile236Ser | missense_variant | 8/9 | ENST00000518322.6 | NP_660312.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CIBAR1 | ENST00000518322.6 | c.707T>G | p.Ile236Ser | missense_variant | 8/9 | 5 | NM_145269.5 | ENSP00000429367 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00171 AC: 260AN: 152218Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000414 AC: 103AN: 249038Hom.: 0 AF XY: 0.000281 AC XY: 38AN XY: 135126
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GnomAD4 exome AF: 0.000148 AC: 217AN: 1461380Hom.: 0 Cov.: 31 AF XY: 0.000127 AC XY: 92AN XY: 726982
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GnomAD4 genome AF: 0.00171 AC: 261AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.00170 AC XY: 127AN XY: 74490
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
CIBAR1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 24, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;T;.;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;.;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;.;D;D;D
REVEL
Benign
Sift
Uncertain
D;D;.;D;D;T
Sift4G
Benign
T;D;D;T;T;D
Polyphen
P;D;.;.;.;.
Vest4
MVP
MPC
ClinPred
T
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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