rs753166385

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_145269.5(CIBAR1):​c.236A>C​(p.Lys79Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,528 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: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

CIBAR1
NM_145269.5 missense

Scores

10
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.37
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CIBAR1NM_145269.5 linkc.236A>C p.Lys79Thr missense_variant Exon 2 of 9 ENST00000518322.6 NP_660312.2 A1XBS5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CIBAR1ENST00000518322.6 linkc.236A>C p.Lys79Thr missense_variant Exon 2 of 9 5 NM_145269.5 ENSP00000429367.1 A1XBS5-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461528
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
727004
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.52
BayesDel_addAF
Uncertain
0.053
T
BayesDel_noAF
Benign
-0.16
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.030
.;T;T;.;T;.;T;.
Eigen
Uncertain
0.19
Eigen_PC
Benign
0.22
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Uncertain
0.90
D;D;D;D;D;D;D;D
M_CAP
Benign
0.035
D
MetaRNN
Uncertain
0.47
T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.88
T
PrimateAI
Uncertain
0.58
T
PROVEAN
Uncertain
-2.8
D;D;D;D;D;D;.;D
REVEL
Benign
0.23
Sift
Benign
0.58
T;T;T;T;T;T;.;T
Sift4G
Uncertain
0.010
D;D;T;T;T;D;T;D
Polyphen
1.0
.;.;D;.;.;.;.;.
Vest4
0.54, 0.56, 0.56, 0.55
MutPred
0.51
.;.;Loss of ubiquitination at K79 (P = 0.0233);Loss of ubiquitination at K79 (P = 0.0233);Loss of ubiquitination at K79 (P = 0.0233);Loss of ubiquitination at K79 (P = 0.0233);Loss of ubiquitination at K79 (P = 0.0233);.;
MVP
0.85
MPC
0.67
ClinPred
0.99
D
GERP RS
3.2
Varity_R
0.23
gMVP
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-94713661; API