dbSNP rs723840: CMTM5:p.Asp184Asp (chr14-23379102-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001288746.2(CMTM5):c.552C>T(p.Asp184Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 1,613,394 control chromosomes in the GnomAD database, including 183,776 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 23899 hom., cov: 31)

Exomes 𝑓: 0.46 ( 159877 hom. )

Consequence

CMTM5
NM_001288746.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.882

Publications

22 publications found

Variant links:

Genes affected

CMTM5 (HGNC:19176): (CKLF like MARVEL transmembrane domain containing 5) This gene encodes a member of the chemokine-like factor superfamily. This family of genes encodes multi-pass membrane proteins that are similar to both the chemokine and the transmembrane 4 superfamilies of signaling molecules. The encoded protein may exhibit tumor suppressor activity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

CMTM5 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BP7

Synonymous conserved (PhyloP=-0.882 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMTM5	NM_001288746.2 link	c.552C>T	p.Asp184Asp	synonymous_variant	Exon 4 of 6	ENST00000339180.9	NP_001275675.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMTM5	ENST00000339180.9 link	c.552C>T	p.Asp184Asp	synonymous_variant	Exon 4 of 6	1	NM_001288746.2	ENSP00000344819.4

Frequencies

GnomAD3 genomes

AF:

0.537

AC:

81601

AN:

151850

Hom.:

23856

Cov.:

show subpopulations

Gnomad AFR

AF:

0.786

Gnomad AMI

AF:

0.406

Gnomad AMR

AF:

0.407

Gnomad ASJ

AF:

0.545

Gnomad EAS

AF:

0.262

Gnomad SAS

AF:

0.470

Gnomad FIN

AF:

0.446

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.457

Gnomad OTH

AF:

0.533

GnomAD2 exomes

AF:

0.444

AC:

111368

AN:

250924

AF XY:

0.447

show subpopulations

Gnomad AFR exome

AF:

0.792

Gnomad AMR exome

AF:

0.271

Gnomad ASJ exome

AF:

0.534

Gnomad EAS exome

AF:

0.254

Gnomad FIN exome

AF:

0.440

Gnomad NFE exome

AF:

0.460

Gnomad OTH exome

AF:

0.465

GnomAD4 exome

AF:

0.461

AC:

673945

AN:

1461426

Hom.:

159877

Cov.:

AF XY:

0.461

AC XY:

335295

AN XY:

727062

show subpopulations

African (AFR)

AF:

0.793

AC:

26559

AN:

33472

American (AMR)

AF:

0.287

AC:

12825

AN:

44696

Ashkenazi Jewish (ASJ)

AF:

0.533

AC:

13929

AN:

26112

East Asian (EAS)

AF:

0.272

AC:

10814

AN:

39698

South Asian (SAS)

AF:

0.477

AC:

41101

AN:

86240

European-Finnish (FIN)

AF:

0.433

AC:

23117

AN:

53374

Middle Eastern (MID)

AF:

0.512

AC:

2951

AN:

5768

European-Non Finnish (NFE)

AF:

0.463

AC:

514355

AN:

1111684

Other (OTH)

AF:

0.469

AC:

28294

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

20160

40320

60479

80639

100799

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15386

30772

46158

61544

76930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.538

AC:

81699

AN:

151968

Hom.:

23899

Cov.:

AF XY:

0.533

AC XY:

39601

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.786

AC:

32582

AN:

41436

American (AMR)

AF:

0.406

AC:

6207

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.545

AC:

1893

AN:

3472

East Asian (EAS)

AF:

0.263

AC:

1354

AN:

5150

South Asian (SAS)

AF:

0.470

AC:

2260

AN:

4812

European-Finnish (FIN)

AF:

0.446

AC:

4714

AN:

10566

Middle Eastern (MID)

AF:

0.524

AC:

154

AN:

294

European-Non Finnish (NFE)

AF:

0.457

AC:

31029

AN:

67936

Other (OTH)

AF:

0.538

AC:

1136

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1759

3518

5276

7035

8794

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

684

1368

2052

2736

3420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.503

Hom.:

44379

Bravo

AF:

0.542

Asia WGS

AF:

0.419

AC:

1454

AN:

3478

EpiCase

AF:

0.468

EpiControl

AF:

0.478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

6.8

(source)

DANN

Benign

0.81

PhyloP100

-0.88

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over