Genetic Variant CD36:c.-184+11225A>G (chr7-80613604-A-G) – 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+11225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,010 control chromosomes in the GnomAD database, including 8,837 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as no classification for the single variant (no stars).

Frequency

Genomes: 𝑓 0.34 ( 8837 hom., cov: 33)

Consequence

CD36
ENST00000309881.11 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0620

Publications

38 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:

Genome browser will be placed here

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 (SAS) allele frequency at 95% confidence interval = 0.449 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+11225A>G	intron	N/A	NP_001001547.1
CD36	NM_001371074.1	c.-180+11225A>G	intron	N/A	NP_001358003.1
CD36	NM_001371075.1	c.-184+11225A>G	intron	N/A	NP_001358004.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD36	ENST00000309881.11	TSL:1	c.-184+11225A>G	intron	N/A	ENSP00000308165.7
CD36	ENST00000435819.5	TSL:2	c.-183-32484A>G	intron	N/A	ENSP00000399421.1
CD36	ENST00000534394.5	TSL:2	c.-109+11225A>G	intron	N/A	ENSP00000431296.1

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

51094

AN:

151892

Hom.:

8830

Cov.:

show subpopulations

Gnomad AFR

AF:

0.270

Gnomad AMI

AF:

0.468

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.350

Gnomad SAS

AF:

0.467

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.364

Gnomad OTH

AF:

0.344

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

GnomAD4 genome

AF:

0.336

AC:

51128

AN:

152010

Hom.:

8837

Cov.:

AF XY:

0.340

AC XY:

25229

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.270

AC:

11222

AN:

41504

American (AMR)

AF:

0.300

AC:

4584

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.347

AC:

1202

AN:

3464

East Asian (EAS)

AF:

0.350

AC:

1809

AN:

5170

South Asian (SAS)

AF:

0.466

AC:

2242

AN:

4816

European-Finnish (FIN)

AF:

0.386

AC:

4080

AN:

10566

Middle Eastern (MID)

AF:

0.411

AC:

120

AN:

292

European-Non Finnish (NFE)

AF:

0.364

AC:

24706

AN:

67890

Other (OTH)

AF:

0.349

AC:

736

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1727

3453

5180

6906

8633

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

522

1044

1566

2088

2610

<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:

0.335

Hom.:

1055

Bravo

AF:

0.325

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

2.4

(source)

DANN

Benign

0.80

PhyloP100

0.062

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

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over