chr1-230868218-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032800.3(C1orf198):c.295G>A(p.Gly99Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000208 in 1,537,516 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 (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
C1orf198
NM_032800.3 missense
NM_032800.3 missense
Scores
2
2
14
Clinical Significance
Conservation
PhyloP100: 1.54
Genes affected
C1orf198 (HGNC:25900): (chromosome 1 open reading frame 198) Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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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=0.15914336).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C1orf198 | NM_032800.3 | c.295G>A | p.Gly99Arg | missense_variant | 1/4 | ENST00000366663.10 | NP_116189.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1orf198 | ENST00000366663.10 | c.295G>A | p.Gly99Arg | missense_variant | 1/4 | 1 | NM_032800.3 | ENSP00000355623 | P1 | |
ENST00000439341.2 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 152006Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000597 AC: 8AN: 134084Hom.: 0 AF XY: 0.0000535 AC XY: 4AN XY: 74736
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GnomAD4 exome AF: 0.0000180 AC: 25AN: 1385402Hom.: 0 Cov.: 34 AF XY: 0.0000204 AC XY: 14AN XY: 684794
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74372
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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 submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | The c.295G>A (p.G99R) alteration is located in exon 1 (coding exon 1) of the C1orf198 gene. This alteration results from a G to A substitution at nucleotide position 295, causing the glycine (G) at amino acid position 99 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D;T
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;N;N
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;D;D
Sift4G
Benign
T;D;.
Polyphen
D;.;.
Vest4
MutPred
Loss of methylation at R98 (P = 0.0353);.;.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at