Genetic Variant CD36:c.-184+21688T>C (chr7-80624067-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000309881.11(CD36):c.-184+21688T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,000 control chromosomes in the GnomAD database, including 9,256 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 0.35 ( 9255 hom., cov: 32)

Exomes 𝑓: 0.33 ( 1 hom. )

Consequence

CD36
ENST00000309881.11 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0760

Publications

16 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000309881.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
CD36	NM_001001547.3	c.-184+21688T>C	intron	N/A	NP_001001547.1
CD36	NM_001371074.1	c.-180+21688T>C	intron	N/A	NP_001358003.1
CD36	NM_001371075.1	c.-184+21688T>C	intron	N/A	NP_001358004.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD36	ENST00000309881.11	TSL:1	c.-184+21688T>C	intron	N/A	ENSP00000308165.7
CD36	ENST00000478292.2	TSL:5	n.173T>C	non_coding_transcript_exon	Exon 1 of 2
CD36	ENST00000435819.5	TSL:2	c.-183-22021T>C	intron	N/A	ENSP00000399421.1

Frequencies

GnomAD3 genomes

AF:

0.347

AC:

52695

AN:

151872

Hom.:

9257

Cov.:

show subpopulations

Gnomad AFR

AF:

0.319

Gnomad AMI

AF:

0.466

Gnomad AMR

AF:

0.314

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.448

Gnomad FIN

AF:

0.385

Gnomad MID

AF:

0.414

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.345

GnomAD4 exome

AF:

0.333

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.750

AC:

AN:

European-Non Finnish (NFE)

AF:

0.167

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.347

AC:

52716

AN:

151988

Hom.:

9255

Cov.:

AF XY:

0.349

AC XY:

25900

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.319

AC:

13211

AN:

41472

American (AMR)

AF:

0.313

AC:

4780

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.347

AC:

1199

AN:

3460

East Asian (EAS)

AF:

0.240

AC:

1235

AN:

5156

South Asian (SAS)

AF:

0.447

AC:

2147

AN:

4808

European-Finnish (FIN)

AF:

0.385

AC:

4068

AN:

10570

Middle Eastern (MID)

AF:

0.408

AC:

119

AN:

292

European-Non Finnish (NFE)

AF:

0.365

AC:

24794

AN:

67958

Other (OTH)

AF:

0.350

AC:

740

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1769

3537

5306

7074

8843

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

530

1060

1590

2120

2650

<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:

0.191

Hom.:

357

Bravo

AF:

0.338

Asia WGS

AF:

0.347

AC:

1205

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

0.076

PromoterAI

0.0034

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over