dbSNP rs2366855: CD36:c.-184+21760T>A (chr7-80624139-T-A) – 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+21760T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,054 control chromosomes in the GnomAD database, including 16,727 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 0.45 ( 16726 hom., cov: 32)

Exomes 𝑓: 0.75 ( 1 hom. )

Consequence

CD36
ENST00000309881.11 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.830

Publications

9 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 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_001371077.1	c.-235T>A	5_prime_UTR	Exon 1 of 15	NP_001358006.1
CD36	NM_001371078.1	c.-235T>A	5_prime_UTR	Exon 1 of 14	NP_001358007.1
CD36	NM_001001547.3	c.-184+21760T>A	intron	N/A	NP_001001547.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD36	ENST00000309881.11	TSL:1	c.-184+21760T>A	intron	N/A	ENSP00000308165.7
CD36	ENST00000478292.2	TSL:5	n.245T>A	non_coding_transcript_exon	Exon 1 of 2
CD36	ENST00000438020.5	TSL:2	c.-235T>A	5_prime_UTR	Exon 1 of 5	ENSP00000410371.1

Frequencies

GnomAD3 genomes

AF:

0.455

AC:

69088

AN:

151932

Hom.:

16724

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.507

Gnomad AMR

AF:

0.508

Gnomad ASJ

AF:

0.546

Gnomad EAS

AF:

0.314

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.530

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.541

Gnomad OTH

AF:

0.484

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

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)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.455

AC:

69110

AN:

152050

Hom.:

16726

Cov.:

AF XY:

0.452

AC XY:

33583

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.300

AC:

12462

AN:

41500

American (AMR)

AF:

0.508

AC:

7749

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.546

AC:

1892

AN:

3466

East Asian (EAS)

AF:

0.315

AC:

1629

AN:

5166

South Asian (SAS)

AF:

0.289

AC:

1394

AN:

4826

European-Finnish (FIN)

AF:

0.530

AC:

5606

AN:

10576

Middle Eastern (MID)

AF:

0.521

AC:

152

AN:

292

European-Non Finnish (NFE)

AF:

0.541

AC:

36758

AN:

67950

Other (OTH)

AF:

0.479

AC:

1007

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1841

3681

5522

7362

9203

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

632

1264

1896

2528

3160

<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.:

1189

Bravo

AF:

0.453

Asia WGS

AF:

0.283

AC:

987

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.0

(source)

DANN

Benign

0.63

PhyloP100

-0.83

PromoterAI

-0.013

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