dbSNP rs1050572: CD200:p.Thr193Thr (chr3-112347715-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005944.7(CD200):c.579G>A(p.Thr193Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,613,630 control chromosomes in the GnomAD database, including 12,039 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 0.15 ( 2362 hom., cov: 32)

Exomes 𝑓: 0.098 ( 9677 hom. )

Consequence

CD200
NM_005944.7 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.70

Publications

11 publications found

Variant links:

Genes affected

CD200 (HGNC:7203): (CD200 molecule) This gene encodes a type I membrane glycoprotein containing two extracellular immunoglobulin domains, a transmembrane and a cytoplasmic domain. This gene is expressed by various cell types, including B cells, a subset of T cells, thymocytes, endothelial cells, and neurons. The encoded protein plays an important role in immunosuppression and regulation of anti-tumor activity. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

CD200 links:

ENSG00000243081 (HGNC:):

ENSG00000243081 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP7

Synonymous conserved (PhyloP=-1.7 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD200	NM_005944.7 link	c.579G>A	p.Thr193Thr	synonymous_variant	Exon 4 of 6	ENST00000315711.12	NP_005935.4	P41217-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD200	ENST00000315711.12 link	c.579G>A	p.Thr193Thr	synonymous_variant	Exon 4 of 6	1	NM_005944.7	ENSP00000312766.8		P41217-2

Frequencies

GnomAD3 genomes

AF:

0.149

AC:

22600

AN:

151842

Hom.:

2342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.288

Gnomad AMI

AF:

0.0407

Gnomad AMR

AF:

0.0950

Gnomad ASJ

AF:

0.0611

Gnomad EAS

AF:

0.230

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0756

Gnomad OTH

AF:

0.120

GnomAD2 exomes

AF:

0.128

AC:

32094

AN:

251358

AF XY:

0.131

show subpopulations

Gnomad AFR exome

AF:

0.293

Gnomad AMR exome

AF:

0.0803

Gnomad ASJ exome

AF:

0.0610

Gnomad EAS exome

AF:

0.233

Gnomad FIN exome

AF:

0.0965

Gnomad NFE exome

AF:

0.0793

Gnomad OTH exome

AF:

0.0984

GnomAD4 exome

AF:

0.0978

AC:

142881

AN:

1461672

Hom.:

9677

Cov.:

AF XY:

0.102

AC XY:

74047

AN XY:

727144

show subpopulations

African (AFR)

AF:

0.302

AC:

10116

AN:

33466

American (AMR)

AF:

0.0806

AC:

3602

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.0602

AC:

1574

AN:

26130

East Asian (EAS)

AF:

0.211

AC:

8363

AN:

39698

South Asian (SAS)

AF:

0.254

AC:

21907

AN:

86248

European-Finnish (FIN)

AF:

0.100

AC:

5344

AN:

53416

Middle Eastern (MID)

AF:

0.115

AC:

661

AN:

5768

European-Non Finnish (NFE)

AF:

0.0760

AC:

84538

AN:

1111844

Other (OTH)

AF:

0.112

AC:

6776

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

6923

13847

20770

27694

34617

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3472

6944

10416

13888

17360

<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:

0.149

AC:

22662

AN:

151958

Hom.:

2362

Cov.:

AF XY:

0.152

AC XY:

11255

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.288

AC:

11932

AN:

41400

American (AMR)

AF:

0.0952

AC:

1454

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0611

AC:

212

AN:

3468

East Asian (EAS)

AF:

0.228

AC:

1179

AN:

5160

South Asian (SAS)

AF:

0.273

AC:

1312

AN:

4806

European-Finnish (FIN)

AF:

0.105

AC:

1103

AN:

10554

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0756

AC:

5139

AN:

67976

Other (OTH)

AF:

0.126

AC:

266

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

914

1828

2743

3657

4571

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

252

504

756

1008

1260

<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:

0.100

Hom.:

5029

Bravo

AF:

0.153

Asia WGS

AF:

0.282

AC:

980

AN:

3478

EpiCase

AF:

0.0765

EpiControl

AF:

0.0837

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.058

(source)

DANN

Benign

0.30

PhyloP100

-1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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