8-93705000-G-C
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_145269.5(CIBAR1):āc.422G>Cā(p.Arg141Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,610,536 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.000033 ( 0 hom., cov: 32)
Exomes š: 0.0000096 ( 0 hom. )
Consequence
CIBAR1
NM_145269.5 missense
NM_145269.5 missense
Scores
5
9
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.90
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248354Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134754
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GnomAD4 exome AF: 0.00000960 AC: 14AN: 1458382Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 725676
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74340
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;T;T;.;T;.;T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D
MetaSVM
Uncertain
T
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D;D;D;.;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;D;D;D;.;D
Sift4G
Uncertain
D;D;D;D;D;D;D;D
Polyphen
1.0
.;.;D;.;.;.;.;.
Vest4
0.81, 0.69, 0.82, 0.74
MutPred
0.58
.;.;Loss of MoRF binding (P = 7e-04);Loss of MoRF binding (P = 7e-04);.;Loss of MoRF binding (P = 7e-04);Loss of MoRF binding (P = 7e-04);.;
MVP
MPC
0.75
ClinPred
D
GERP RS
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