rs3211913

Variant names:

Variant summary

Our verdict is The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The NM_001001548.3(CD36):c.701+791A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.124 (AC=18,789) in the gnomAD database across 151,914 control chromosomes, including 2,803 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.35. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 2803 hom., cov: 32)

Consequence

CD36
NM_001001548.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.939

Publications

7 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

new If you want to explore the variant's impact on the transcript NM_001001548.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

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

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); Splicing verdict: benign (Strong).; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.3499 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_001001548.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD36	NM_001001548.3	MANE Select	c.701+791A>G	intron	N/A	NP_001001548.1	P16671-1
CD36	NM_000072.3		c.701+791A>G	intron	N/A	NP_000063.2	P16671-1
CD36	NM_001001547.3		c.701+791A>G	intron	N/A	NP_001001547.1	A4D1B1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD36	ENST00000447544.7	TSL:5 MANE Select	c.701+791A>G	intron	N/A	ENSP00000415743.2	P16671-1
CD36	ENST00000309881.11	TSL:1	c.701+791A>G	intron	N/A	ENSP00000308165.7	P16671-1
CD36	ENST00000394788.7	TSL:1	c.701+791A>G	intron	N/A	ENSP00000378268.3	P16671-1

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18724

AN:

151798

Hom.:

2783

Cov.:

show subpopulations

Gnomad AFR

AF:

0.354

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0890

Gnomad ASJ

AF:

0.0447

Gnomad EAS

AF:

0.0879

Gnomad SAS

AF:

0.0248

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0238

Gnomad OTH

AF:

0.0917

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

GnomAD4 genome

AF:

0.124

AC:

18789

AN:

151914

Hom.:

2803

Cov.:

AF XY:

0.121

AC XY:

8977

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.355

AC:

14671

AN:

41360

American (AMR)

AF:

0.0896

AC:

1365

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.0447

AC:

155

AN:

3464

East Asian (EAS)

AF:

0.0881

AC:

455

AN:

5162

South Asian (SAS)

AF:

0.0251

AC:

121

AN:

4828

European-Finnish (FIN)

AF:

0.0185

AC:

196

AN:

10580

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0238

AC:

1618

AN:

67966

Other (OTH)

AF:

0.0907

AC:

191

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

654

1309

1963

2618

3272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

170

340

510

680

850

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

TOPMed (Bravo)

AF:

0.141

ALFA (dbGaP/dbSNP Allele Frequency Aggregator)

AF:

0.0926

AC:

3583

AN:

38714

Hom.:

450

Local populations

ABraOM SABE-WGS-1171

AF:

0.118

AC:

276

AN:

2342

Hom.:

ChinaMAP Phase 1

AF:

0.0744

Denmark Genome

AF:

0.0300

AC:

AN:

300

GenomeAsia100K

AF:

0.0740

AC:

256

AN:

3450

show subpopulations

Oceania

AF:

0.00

AC:

AN:

148

Hom.:

North-East Asia

AF:

0.0741

AC:

AN:

702

Hom.:

South-East Asia

AF:

0.103

AC:

AN:

692

Hom.:

South Asia

AF:

0.0296

AC:

AN:

1420

Hom.:

Africa

AF:

0.380

AC:

AN:

208

Hom.:

America

AF:

0.154

AC:

AN:

Hom.:

West Eurasia

AF:

0.0175

AC:

AN:

228

Hom.:

Korea4K (4,157 Koreans)

AF:

0.0860

AC:

620

AN:

7218

Qatari Genome

AF:

0.102

AC:

AN:

176

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.130

AC:

15837

AN:

121740

Hom.:

1029

Turkish Variome

AF:

0.0233

AC:

AN:

1546

Hom.:

UK10K

AF:

0.0206

AC:

156

AN:

7562

show subpopulations

TwinsUK

AF:

0.0193

AC:

AN:

3574

ALSPAC

AF:

0.0221

AC:

AN:

3854

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.0807

AC:

723

AN:

8960

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.80

(source)

DANN

Benign

0.77

PhyloP100

-0.94

AlphaGenome AVI

Benign

1.7

(source)

GPN-Star LLR

3.8

(source)

GPN-Star score

-0.51

(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

Pangolin (max)

Benign

0.0

(source)

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over