Genetic Variant NM_005944.7:c.579G>A (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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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