1-172468452-G-T

Variant summary

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

The ENST00000367727.9(C1orf105):​c.410G>T​(p.Ser137Ile) 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. 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. S137N) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

C1orf105
ENST00000367727.9 missense

Scores

1
3
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.313
Variant links:
Genes affected
C1orf105 (HGNC:29591): (chromosome 1 open reading frame 105)

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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=0.23810962).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
C1orf105NM_139240.4 linkuse as main transcriptc.410G>T p.Ser137Ile missense_variant 7/7 ENST00000367727.9 NP_640333.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
C1orf105ENST00000367727.9 linkuse as main transcriptc.410G>T p.Ser137Ile missense_variant 7/71 NM_139240.4 ENSP00000356700 P1
C1orf105ENST00000367725.4 linkuse as main transcriptc.380G>T p.Ser127Ile missense_variant 5/52 ENSP00000356698
C1orf105ENST00000367726.1 linkuse as main transcriptn.214G>T non_coding_transcript_exon_variant 4/43

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
37
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.27
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
15
DANN
Uncertain
0.98
DEOGEN2
Benign
0.031
T;.
Eigen
Benign
-0.28
Eigen_PC
Benign
-0.45
FATHMM_MKL
Benign
0.094
N
LIST_S2
Benign
0.65
T;T
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.24
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.90
L;.
MutationTaster
Benign
1.0
N;N
PROVEAN
Pathogenic
-5.1
D;D
REVEL
Benign
0.19
Sift
Uncertain
0.0030
D;D
Sift4G
Uncertain
0.0040
D;D
Polyphen
0.99
D;.
Vest4
0.37
MutPred
0.30
Loss of disorder (P = 0.0213);.;
MVP
0.40
MPC
0.16
ClinPred
0.95
D
GERP RS
1.1
Varity_R
0.40
gMVP
0.092

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
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: rs1129942; hg19: chr1-172437592; API