NM_001164310.3:c.538A>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001164310.3(CIMIP2B):​c.538A>C​(p.Met180Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

CIMIP2B
NM_001164310.3 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.581
Variant links:
Genes affected
CIMIP2B (HGNC:34242): (ciliary microtubule inner protein 2B)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.14807537).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CIMIP2BNM_001164310.3 linkc.538A>C p.Met180Leu missense_variant Exon 4 of 6 ENST00000399742.7 NP_001157782.1 A8MTA8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM166BENST00000399742.7 linkc.538A>C p.Met180Leu missense_variant Exon 4 of 6 1 NM_001164310.3 ENSP00000382646.2 A8MTA8-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
35
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.21
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
18
DANN
Benign
0.92
DEOGEN2
Benign
0.0095
.;T;.
Eigen
Benign
-0.088
Eigen_PC
Benign
-0.042
FATHMM_MKL
Benign
0.59
D
LIST_S2
Benign
0.54
T;T;T
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.15
T;T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Uncertain
2.5
.;M;M
PrimateAI
Benign
0.45
T
PROVEAN
Benign
-1.4
.;N;.
REVEL
Benign
0.10
Sift
Benign
0.28
.;T;.
Sift4G
Benign
0.40
T;T;.
Polyphen
0.17, 0.42
.;B;B
Vest4
0.36
MutPred
0.41
Loss of disorder (P = 0.108);Loss of disorder (P = 0.108);Loss of disorder (P = 0.108);
MVP
0.12
MPC
0.064
ClinPred
0.37
T
GERP RS
2.8
Varity_R
0.15
gMVP
0.45

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs764534873; hg19: chr9-35562652; API