chr3-32391961-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_138410.4(CMTM7):āc.55G>Cā(p.Gly19Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000268 in 1,231,282 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 (ā ).
Frequency
Genomes: š 0.00015 ( 0 hom., cov: 33)
Exomes š: 0.0000093 ( 0 hom. )
Consequence
CMTM7
NM_138410.4 missense
NM_138410.4 missense
Scores
2
2
15
Clinical Significance
Conservation
PhyloP100: 1.55
Genes affected
CMTM7 (HGNC:19178): (CKLF like MARVEL transmembrane domain containing 7) This gene belongs to the chemokine-like factor gene superfamily, a novel family that is similar to the chemokine and transmembrane 4 superfamilies. This gene is one of several chemokine-like factor genes located in a cluster on chromosome 3. This gene acts as a tumor suppressor that regulates G1/S transition in the cell cycle, and epidermal growth factor receptor/protein kinase B signaling during tumor pathogenesis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2645557).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CMTM7 | NM_138410.4 | c.55G>C | p.Gly19Arg | missense_variant | 1/5 | ENST00000334983.10 | |
CMTM7 | NM_181472.3 | c.55G>C | p.Gly19Arg | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CMTM7 | ENST00000334983.10 | c.55G>C | p.Gly19Arg | missense_variant | 1/5 | 1 | NM_138410.4 | P1 | |
CMTM7 | ENST00000349718.8 | c.55G>C | p.Gly19Arg | missense_variant | 1/4 | 1 | |||
CMTM7 | ENST00000454304.6 | c.55G>C | p.Gly19Arg | missense_variant, NMD_transcript_variant | 1/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152056Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000927 AC: 10AN: 1079226Hom.: 0 Cov.: 32 AF XY: 0.0000137 AC XY: 7AN XY: 509918
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GnomAD4 genome AF: 0.000151 AC: 23AN: 152056Hom.: 0 Cov.: 33 AF XY: 0.000162 AC XY: 12AN XY: 74282
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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 | Jul 26, 2022 | The c.55G>C (p.G19R) alteration is located in exon 1 (coding exon 1) of the CMTM7 gene. This alteration results from a G to C substitution at nucleotide position 55, causing the glycine (G) at amino acid position 19 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
N;N
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;D
Sift4G
Benign
T;T
Polyphen
P;.
Vest4
MutPred
Gain of MoRF binding (P = 0.0153);Gain of MoRF binding (P = 0.0153);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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