16-66622114-G-A

Variant summary

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

The NM_181521.3(CMTM4):​c.571C>T​(p.Arg191Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000885 in 1,604,278 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 0.000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000091 ( 0 hom. )

Consequence

CMTM4
NM_181521.3 missense

Scores

2
9
8

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.15
Variant links:
Genes affected
CMTM4 (HGNC:19175): (CKLF like MARVEL transmembrane domain containing 4) This gene belongs to the chemokine-like factor gene superfamily, a novel family that is similar to the chemokine and the transmembrane 4 superfamilies of signaling molecules. This gene is one of several chemokine-like factor genes located in a cluster on chromosome 16. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

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=0.21860233).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CMTM4NM_181521.3 linkc.571C>T p.Arg191Cys missense_variant 4/4 ENST00000394106.7 NP_852662.1 Q8IZR5-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CMTM4ENST00000394106.7 linkc.571C>T p.Arg191Cys missense_variant 4/41 NM_181521.3 ENSP00000377666.2 Q8IZR5-2
CMTM4ENST00000330687.8 linkc.571C>T p.Arg191Cys missense_variant 4/51 ENSP00000333833.4 Q8IZR5-1
CMTM4ENST00000563952.1 linkc.484C>T p.Arg162Cys missense_variant 4/41 ENSP00000456380.1 Q8IZR5-3
CMTM4ENST00000561680.5 linkc.289C>T p.Arg97Cys missense_variant 3/52 ENSP00000464316.1 J3QRP2

Frequencies

GnomAD3 genomes
AF:
0.0000657
AC:
10
AN:
152214
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000723
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000161
AC:
38
AN:
235518
Hom.:
0
AF XY:
0.000205
AC XY:
26
AN XY:
126960
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000911
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000566
Gnomad SAS exome
AF:
0.000771
Gnomad FIN exome
AF:
0.0000489
Gnomad NFE exome
AF:
0.000104
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000909
AC:
132
AN:
1452064
Hom.:
0
Cov.:
33
AF XY:
0.000119
AC XY:
86
AN XY:
721192
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000694
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.000853
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000470
Gnomad4 OTH exome
AF:
0.0000499
GnomAD4 genome
AF:
0.0000657
AC:
10
AN:
152214
Hom.:
0
Cov.:
33
AF XY:
0.0000269
AC XY:
2
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.0000723
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000103
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000772
Hom.:
0
Bravo
AF:
0.0000453
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000519
AC:
2
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.000107
AC:
13

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 GeneticsOct 12, 2024The c.571C>T (p.R191C) alteration is located in exon 4 (coding exon 4) of the CMTM4 gene. This alteration results from a C to T substitution at nucleotide position 571, causing the arginine (R) at amino acid position 191 to be replaced by a cysteine (C). 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
Uncertain
0.51
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Benign
-0.10
CADD
Pathogenic
33
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.14
T;T;.;.
Eigen
Uncertain
0.65
Eigen_PC
Pathogenic
0.72
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Uncertain
0.95
D;D;D;D
M_CAP
Benign
0.020
T
MetaRNN
Benign
0.22
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.5
L;.;L;.
PrimateAI
Uncertain
0.68
T
PROVEAN
Uncertain
-2.4
N;.;N;D
REVEL
Uncertain
0.35
Sift
Uncertain
0.0050
D;.;D;D
Sift4G
Uncertain
0.0050
D;D;D;D
Polyphen
1.0
D;.;.;.
Vest4
0.75
MVP
0.50
MPC
1.6
ClinPred
0.19
T
GERP RS
6.1
Varity_R
0.13
gMVP
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs374010185; hg19: chr16-66656017; API