rs865999990

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_014895.4(CEP162):​c.3848G>T​(p.Arg1283Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000141 in 1,417,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1283Q) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

CEP162
NM_014895.4 missense

Scores

5
9
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.28
Variant links:
Genes affected
CEP162 (HGNC:21107): (centrosomal protein 162) Involved in cilium assembly. Located in axonemal microtubule; centriole; and centrosome. [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 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.747

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CEP162NM_014895.4 linkc.3848G>T p.Arg1283Leu missense_variant Exon 25 of 27 ENST00000403245.8 NP_055710.2 Q5TB80-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CEP162ENST00000403245.8 linkc.3848G>T p.Arg1283Leu missense_variant Exon 25 of 27 5 NM_014895.4 ENSP00000385215.3 Q5TB80-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000141
AC:
2
AN:
1417052
Hom.:
0
Cov.:
27
AF XY:
0.00000142
AC XY:
1
AN XY:
701972
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000519
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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.79
BayesDel_addAF
Pathogenic
0.21
D
BayesDel_noAF
Uncertain
0.060
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Benign
0.25
.;T;.
Eigen
Uncertain
0.66
Eigen_PC
Pathogenic
0.67
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.90
.;D;D
M_CAP
Benign
0.063
D
MetaRNN
Pathogenic
0.75
D;D;D
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.4
.;M;.
PrimateAI
Uncertain
0.53
T
PROVEAN
Uncertain
-3.6
D;D;.
REVEL
Uncertain
0.39
Sift
Uncertain
0.0050
D;D;.
Sift4G
Benign
0.061
T;D;T
Polyphen
0.94
.;P;.
Vest4
0.80
MutPred
0.33
.;Loss of loop (P = 0.1258);.;
MVP
0.29
MPC
0.11
ClinPred
1.0
D
GERP RS
5.8
Varity_R
0.49
gMVP
0.49

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs865999990; hg19: chr6-84856428; API