rs557635896

Variant summary

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

The NM_001080503.3(CCDC159):​c.292C>G​(p.Arg98Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,399,544 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. R98P) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 31)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

CCDC159
NM_001080503.3 missense

Scores

2
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.107
Variant links:
Genes affected
CCDC159 (HGNC:26996): (coiled-coil domain containing 159)

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=0.13711151).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC159NM_001080503.3 linkc.292C>G p.Arg98Gly missense_variant Exon 5 of 11 ENST00000458408.6 NP_001073972.2 P0C7I6-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC159ENST00000458408.6 linkc.292C>G p.Arg98Gly missense_variant Exon 5 of 11 5 NM_001080503.3 ENSP00000402239.1 P0C7I6-2

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
0.00000143
AC:
2
AN:
1399544
Hom.:
0
Cov.:
32
AF XY:
0.00000290
AC XY:
2
AN XY:
690396
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:
0.0000126
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.26e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.17
T
BayesDel_noAF
Benign
-0.49
CADD
Benign
17
DANN
Uncertain
0.99
Eigen
Benign
-0.35
Eigen_PC
Benign
-0.36
FATHMM_MKL
Benign
0.26
N
LIST_S2
Benign
0.45
.;T;T;T;T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.14
T;T;T;T;T
MetaSVM
Benign
-1.0
T
PrimateAI
Benign
0.22
T
PROVEAN
Uncertain
-3.5
.;D;.;.;.
REVEL
Benign
0.065
Sift
Benign
0.077
.;T;.;.;.
Sift4G
Benign
0.11
T;T;T;T;T
Vest4
0.22
MVP
0.17
MPC
0.23
ClinPred
0.66
D
GERP RS
4.0
Varity_R
0.28
gMVP
0.14

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs557635896; hg19: chr19-11461549; API