3-50565527-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000357203.8(C3orf18):​c.173G>T​(p.Gly58Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

C3orf18
ENST00000357203.8 missense

Scores

4
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.47
Variant links:
Genes affected
C3orf18 (HGNC:24837): (chromosome 3 open reading frame 18) Predicted to be integral component of membrane. [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 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
C3orf18NM_016210.5 linkuse as main transcriptc.173G>T p.Gly58Val missense_variant 3/6 ENST00000357203.8 NP_057294.2 Q9UK00-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
C3orf18ENST00000357203.8 linkuse as main transcriptc.173G>T p.Gly58Val missense_variant 3/61 NM_016210.5 ENSP00000349732.3 Q9UK00-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsNov 09, 2021The c.173G>T (p.G58V) alteration is located in exon 3 (coding exon 1) of the C3orf18 gene. This alteration results from a G to T substitution at nucleotide position 173, causing the glycine (G) at amino acid position 58 to be replaced by a valine (V). 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
Benign
0.15
BayesDel_addAF
Benign
-0.058
T
BayesDel_noAF
Benign
-0.32
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.12
T;T;T;.
Eigen
Benign
0.17
Eigen_PC
Benign
0.093
FATHMM_MKL
Benign
0.71
D
LIST_S2
Benign
0.73
.;.;T;T
M_CAP
Benign
0.023
T
MetaRNN
Uncertain
0.48
T;T;T;D
MetaSVM
Benign
-0.92
T
MutationAssessor
Uncertain
2.2
M;M;M;M
MutationTaster
Benign
1.0
D;D;D;D
PROVEAN
Benign
-1.5
N;N;N;N
REVEL
Benign
0.14
Sift
Uncertain
0.022
D;D;D;T
Sift4G
Benign
0.091
T;T;T;T
Polyphen
0.99
D;D;D;.
Vest4
0.58
MutPred
0.31
Gain of sheet (P = 0.0125);Gain of sheet (P = 0.0125);Gain of sheet (P = 0.0125);Gain of sheet (P = 0.0125);
MVP
0.42
MPC
0.50
ClinPred
0.90
D
GERP RS
4.2
Varity_R
0.14
gMVP
0.68

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-50602958; API