8-93726443-T-G

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6

The NM_145269.5(CIBAR1):ā€‹c.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

Scores

2
8
8

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 4.51
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]

Genome browser will be placed here

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
CIBAR1NM_145269.5 linkuse as main transcriptc.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
CIBAR1ENST00000518322.6 linkuse as main transcriptc.707T>G p.Ile236Ser missense_variant 8/95 NM_145269.5 ENSP00000429367 P1A1XBS5-1

Frequencies

GnomAD3 genomes
AF:
0.00171
AC:
260
AN:
152218
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00586
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000589
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.000414
AC:
103
AN:
249038
Hom.:
0
AF XY:
0.000281
AC XY:
38
AN XY:
135126
show subpopulations
Gnomad AFR exome
AF:
0.00601
Gnomad AMR exome
AF:
0.000261
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000165
GnomAD4 exome
AF:
0.000148
AC:
217
AN:
1461380
Hom.:
0
Cov.:
31
AF XY:
0.000127
AC XY:
92
AN XY:
726982
show subpopulations
Gnomad4 AFR exome
AF:
0.00544
Gnomad4 AMR exome
AF:
0.000246
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.000348
GnomAD4 genome
AF:
0.00171
AC:
261
AN:
152336
Hom.:
0
Cov.:
32
AF XY:
0.00170
AC XY:
127
AN XY:
74490
show subpopulations
Gnomad4 AFR
AF:
0.00587
Gnomad4 AMR
AF:
0.000588
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00236
Alfa
AF:
0.000604
Hom.:
0
Bravo
AF:
0.00188
ESP6500AA
AF:
0.00510
AC:
19
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000530
AC:
64

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 providedclinical testingPreventionGenetics, part of Exact SciencesDec 24, 2019This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.70
BayesDel_addAF
Benign
-0.030
T
BayesDel_noAF
Pathogenic
0.19
CADD
Uncertain
26
DANN
Uncertain
0.99
DEOGEN2
Benign
0.098
T;.;T;.;.;T
Eigen
Uncertain
0.67
Eigen_PC
Uncertain
0.66
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Uncertain
0.95
D;D;D;.;D;D
M_CAP
Benign
0.026
D
MetaRNN
Benign
0.011
T;T;T;T;T;T
MetaSVM
Benign
-0.41
T
MutationTaster
Benign
1.0
D;D;D;D;D
PrimateAI
Uncertain
0.50
T
PROVEAN
Uncertain
-2.6
D;D;.;D;D;D
REVEL
Benign
0.27
Sift
Uncertain
0.017
D;D;.;D;D;T
Sift4G
Benign
0.11
T;D;D;T;T;D
Polyphen
0.95
P;D;.;.;.;.
Vest4
0.76
MVP
0.78
MPC
0.23
ClinPred
0.096
T
GERP RS
5.5
Varity_R
0.51
gMVP
0.53

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.16
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs148804292; hg19: chr8-94738671; API