8-93718773-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_145269.5(CIBAR1):ā€‹c.642A>Cā€‹(p.Glu214Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000714 in 1,399,828 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 Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 7.1e-7 ( 0 hom. )

Consequence

CIBAR1
NM_145269.5 missense

Scores

6
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.68
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 Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.37837106).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CIBAR1NM_145269.5 linkc.642A>C p.Glu214Asp missense_variant Exon 7 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.642A>C p.Glu214Asp missense_variant Exon 7 of 9 5 NM_145269.5 ENSP00000429367.1 A1XBS5-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000546
AC:
1
AN:
183264
Hom.:
0
AF XY:
0.0000103
AC XY:
1
AN XY:
97258
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000383
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:
0.00
GnomAD4 exome
AF:
7.14e-7
AC:
1
AN:
1399828
Hom.:
0
Cov.:
26
AF XY:
0.00000145
AC XY:
1
AN XY:
691496
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000264
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000756

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Sep 08, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.642A>C (p.E214D) alteration is located in exon 7 (coding exon 7) of the FAM92A1 gene. This alteration results from a A to C substitution at nucleotide position 642, causing the glutamic acid (E) at amino acid position 214 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.49
BayesDel_addAF
Benign
-0.036
T
BayesDel_noAF
Benign
-0.17
CADD
Benign
21
DANN
Uncertain
0.99
DEOGEN2
Benign
0.0096
T;T;.;.;T
Eigen
Benign
0.17
Eigen_PC
Benign
0.14
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Uncertain
0.88
D;D;.;D;D
M_CAP
Benign
0.023
T
MetaRNN
Benign
0.38
T;T;T;T;T
MetaSVM
Benign
-0.77
T
PrimateAI
Uncertain
0.55
T
PROVEAN
Benign
-1.4
N;.;N;N;N
REVEL
Uncertain
0.38
Sift
Benign
0.34
T;.;T;T;T
Sift4G
Benign
0.48
T;T;T;T;T
Polyphen
0.99
D;.;.;.;.
Vest4
0.49
MutPred
0.54
Gain of helix (P = 0.132);.;.;.;.;
MVP
0.56
MPC
0.14
ClinPred
0.51
D
GERP RS
2.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.16
gMVP
0.45

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

LitVar

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

Other links and lift over

dbSNP: rs1484945554; hg19: chr8-94731001; API