Genetic Variant CD36:c.-184+7723T>C (chr7-80610102-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000309881.11(CD36):c.-184+7723T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,058 control chromosomes in the GnomAD database, including 12,692 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 0.40 ( 12692 hom., cov: 32)

Consequence

CD36
ENST00000309881.11 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.59

Publications

12 publications found

Variant links:

Genes affected

CD36 (HGNC:1663): (CD36 molecule (CD36 blood group)) The protein encoded by this gene is the fourth major glycoprotein of the platelet surface and serves as a receptor for thrombospondin in platelets and various cell lines. Since thrombospondins are widely distributed proteins involved in a variety of adhesive processes, this protein may have important functions as a cell adhesion molecule. It binds to collagen, thrombospondin, anionic phospholipids and oxidized LDL. It directly mediates cytoadherence of Plasmodium falciparum parasitized erythrocytes and it binds long chain fatty acids and may function in the transport and/or as a regulator of fatty acid transport. Mutations in this gene cause platelet glycoprotein deficiency. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Feb 2014]

CD36 Gene-Disease associations (from GenCC):

platelet-type bleeding disorder 10
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine

CD36 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
CD36	NM_001001547.3 link	c.-184+7723T>C	intron_variant	Intron 1 of 13	NP_001001547.1
CD36	NM_001371074.1 link	c.-180+7723T>C	intron_variant	Intron 1 of 13	NP_001358003.1
CD36	NM_001371075.1 link	c.-184+7723T>C	intron_variant	Intron 1 of 14	NP_001358004.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
CD36	ENST00000309881.11 link	c.-184+7723T>C	intron_variant	Intron 1 of 13	1	ENSP00000308165.7
CD36	ENST00000435819.5 link	c.-183-35986T>C	intron_variant	Intron 4 of 16	2	ENSP00000399421.1
CD36	ENST00000534394.5 link	c.-109+7723T>C	intron_variant	Intron 1 of 11	2	ENSP00000431296.1

Frequencies

GnomAD3 genomes

AF:

0.405

AC:

61489

AN:

151940

Hom.:

12672

Cov.:

show subpopulations

Gnomad AFR

AF:

0.472

Gnomad AMI

AF:

0.473

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.346

Gnomad SAS

AF:

0.470

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.380

Gnomad OTH

AF:

0.391

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.405

AC:

61550

AN:

152058

Hom.:

12692

Cov.:

AF XY:

0.405

AC XY:

30103

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.472

AC:

19566

AN:

41420

American (AMR)

AF:

0.335

AC:

5130

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.382

AC:

1324

AN:

3468

East Asian (EAS)

AF:

0.346

AC:

1789

AN:

5170

South Asian (SAS)

AF:

0.469

AC:

2264

AN:

4826

European-Finnish (FIN)

AF:

0.398

AC:

4207

AN:

10558

Middle Eastern (MID)

AF:

0.449

AC:

132

AN:

294

European-Non Finnish (NFE)

AF:

0.380

AC:

25869

AN:

68002

Other (OTH)

AF:

0.396

AC:

838

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1863

3727

5590

7454

9317

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

584

1168

1752

2336

2920

<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:

0.390

Hom.:

31708

Bravo

AF:

0.400

Asia WGS

AF:

0.420

AC:

1459

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

9.6

(source)

DANN

Benign

0.79

PhyloP100

1.6

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over