Genetic Variant CMTM2:p.Gly86Val (chr16-66579864-G-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_144673.3(CMTM2):c.257G>T(p.Gly86Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000853 in 1,613,948 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00072 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00087 ( 2 hom. )

Consequence

CMTM2
NM_144673.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.71

Variant links:

Genes affected

CMTM2 (HGNC:19173): (CKLF like MARVEL transmembrane domain containing 2) This gene belongs to the chemokine-like factor gene superfamily, a novel family that links the chemokine and the transmembrane 4 superfamilies of signaling molecules. The protein encoded by this gene may play an important role in testicular development. [provided by RefSeq, Jul 2008]

CMTM2 links:

ENSG00000260650 (HGNC:):

ENSG00000260650 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.06745002).

BS2

High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMTM2	NM_144673.3 link	c.257G>T	p.Gly86Val	missense_variant	Exon 1 of 4	ENST00000268595.3	NP_653274.1	Q8TAZ6-1
CMTM2	NM_001199317.2 link	c.257G>T	p.Gly86Val	missense_variant	Exon 1 of 3		NP_001186246.1	Q8TAZ6-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CMTM2	ENST00000268595.3 link	c.257G>T	p.Gly86Val	missense_variant	Exon 1 of 4	1	NM_144673.3	ENSP00000268595.2	Q8TAZ6-1
CMTM2	ENST00000379486.6 link	c.257G>T	p.Gly86Val	missense_variant	Exon 1 of 3	1		ENSP00000368800.2	Q8TAZ6-2
CMTM2	ENST00000569316.1 link	n.91+166G>T		intron_variant	Intron 1 of 3	5		ENSP00000454319.1	H3BMC0
ENSG00000260650	ENST00000568430.1 link	n.*119C>A		downstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.000717

AC:

109

AN:

152128

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000169

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.00131

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000882

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.000570

AC:

143

AN:

250874

Hom.:

AF XY:

0.000567

AC XY:

AN XY:

135796

show subpopulations

Gnomad AFR exome

AF:

0.000249

Gnomad AMR exome

AF:

0.000376

Gnomad ASJ exome

AF:

0.00248

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.000820

Gnomad OTH exome

AF:

0.000983

GnomAD4 exome

AF:

0.000867

AC:

1267

AN:

1461704

Hom.:

Cov.:

AF XY:

0.000817

AC XY:

594

AN XY:

727126

show subpopulations

Gnomad4 AFR exome

AF:

0.000119

Gnomad4 AMR exome

AF:

0.000402

Gnomad4 ASJ exome

AF:

0.00283

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000116

Gnomad4 FIN exome

AF:

0.0000751

Gnomad4 NFE exome

AF:

0.00100

Gnomad4 OTH exome

AF:

0.000679

GnomAD4 genome

AF:

0.000716

AC:

109

AN:

152244

Hom.:

Cov.:

AF XY:

0.000806

AC XY:

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.000168

Gnomad4 AMR

AF:

0.00131

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000882

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.00118

Hom.:

Bravo

AF:

0.000929

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.000682

AC:

ESP6500EA

AF:

0.00140

AC:

ExAC

AF:

0.000502

AC:

EpiCase

AF:

0.00115

EpiControl

AF:

0.00130

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Nov 27, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.257G>T (p.G86V) alteration is located in exon 1 (coding exon 1) of the CMTM2 gene. This alteration results from a G to T substitution at nucleotide position 257, causing the glycine (G) at amino acid position 86 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

Pathogenic

0.67

BayesDel_addAF

Uncertain

0.024

BayesDel_noAF

Pathogenic

0.18

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.11

.;T

Eigen

Uncertain

0.35

Eigen_PC

Uncertain

0.27

FATHMM_MKL

Benign

0.49

LIST_S2

Benign

0.80

T;T

M_CAP

Benign

0.052

MetaRNN

Benign

0.067

T;T

MetaSVM

Uncertain

-0.23

MutationAssessor

Uncertain

2.0

M;M

PrimateAI

Benign

0.46

PROVEAN

Pathogenic

-7.2

D;D

REVEL

Uncertain

0.43

Sift

Uncertain

0.0090

D;T

Sift4G

Pathogenic

0.0

D;D

Polyphen

1.0

.;D

Vest4

0.78

MVP

0.67

MPC

0.88

ClinPred

0.11

GERP RS

4.5

Varity_R

0.71

gMVP

0.23

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over