7-80622979-A-C

Variant summary

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

The ENST00000309881.11(CD36):​c.-184+20600A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 150,608 control chromosomes in the GnomAD database, including 18,280 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 0.49 ( 18280 hom., cov: 30)

Consequence

CD36
ENST00000309881.11 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.196

Publications

6 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

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=-0.87).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CD36NM_001001547.3 linkc.-184+20600A>C intron_variant Intron 1 of 13 NP_001001547.1 P16671-1A4D1B1
CD36NM_001371074.1 linkc.-180+20600A>C intron_variant Intron 1 of 13 NP_001358003.1
CD36NM_001371075.1 linkc.-184+20600A>C intron_variant Intron 1 of 14 NP_001358004.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CD36ENST00000309881.11 linkc.-184+20600A>C intron_variant Intron 1 of 13 1 ENSP00000308165.7 P16671-1
CD36ENST00000435819.5 linkc.-183-23109A>C intron_variant Intron 4 of 16 2 ENSP00000399421.1 P16671-1
CD36ENST00000534394.5 linkc.-109+20600A>C intron_variant Intron 1 of 11 2 ENSP00000431296.1 E9PLT1

Frequencies

GnomAD3 genomes
AF:
0.488
AC:
73470
AN:
150492
Hom.:
18265
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.573
Gnomad AMI
AF:
0.491
Gnomad AMR
AF:
0.432
Gnomad ASJ
AF:
0.423
Gnomad EAS
AF:
0.581
Gnomad SAS
AF:
0.696
Gnomad FIN
AF:
0.456
Gnomad MID
AF:
0.465
Gnomad NFE
AF:
0.437
Gnomad OTH
AF:
0.471
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.488
AC:
73522
AN:
150608
Hom.:
18280
Cov.:
30
AF XY:
0.492
AC XY:
36105
AN XY:
73432
show subpopulations
African (AFR)
AF:
0.572
AC:
23519
AN:
41082
American (AMR)
AF:
0.431
AC:
6482
AN:
15036
Ashkenazi Jewish (ASJ)
AF:
0.423
AC:
1460
AN:
3452
East Asian (EAS)
AF:
0.580
AC:
2964
AN:
5108
South Asian (SAS)
AF:
0.695
AC:
3312
AN:
4768
European-Finnish (FIN)
AF:
0.456
AC:
4648
AN:
10196
Middle Eastern (MID)
AF:
0.462
AC:
134
AN:
290
European-Non Finnish (NFE)
AF:
0.437
AC:
29569
AN:
67694
Other (OTH)
AF:
0.476
AC:
988
AN:
2074
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1852
3703
5555
7406
9258
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
674
1348
2022
2696
3370
<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:
0.460
Hom.:
9267
Bravo
AF:
0.479
Asia WGS
AF:
0.642
AC:
2226
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.8
DANN
Benign
0.79
PhyloP100
-0.20
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs12706912; hg19: chr7-80252295; API