rs3211891

Variant names:

• chr7-80661032-T-C
• rs3211891
• NM_001001548.3:c.282-31T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001001548.3(CD36):​c.282-31T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00329 in 1,541,642 control chromosomes in the GnomAD database, including 138 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 0.017 (74 hom., cov: 33)
  • Exomes 𝑓: 0.0018 (64 hom.)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• Publications: 4 publications found

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

ENSG00000298725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.057 is higher than 0.05.

Variant Effect in Transcripts

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

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001548.3	MANE Select	c.282-31T>C		intron	N/A	NP_001001548.1
	CD36	NM_000072.3		c.282-31T>C		intron	N/A	NP_000063.2
	CD36	NM_001001547.3		c.282-31T>C		intron	N/A	NP_001001547.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.282-31T>C		intron	N/A	ENSP00000415743.2
	CD36	ENST00000309881.11	TSL:1	c.282-31T>C		intron	N/A	ENSP00000308165.7
	CD36	ENST00000394788.7	TSL:1	c.282-31T>C		intron	N/A	ENSP00000378268.3

Frequencies

GnomAD3 genomes AF: 0.0172 AC: 2614 AN: 152194 Hom.: 74 Cov.: 33

Gnomad AFR AF: 0.0588

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00818

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000294

Gnomad OTH AF: 0.0129

GnomAD2 exomes AF: 0.00472 AC: 1182 AN: 250532 AF XY: 0.00349

Gnomad AFR exome AF: 0.0604

Gnomad AMR exome AF: 0.00419

Gnomad ASJ exome AF: 0.000996

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000256

Gnomad OTH exome AF: 0.00164

GnomAD4 exome AF: 0.00176 AC: 2448 AN: 1389330 Hom.: 64 Cov.: 23 AF XY: 0.00151 AC XY: 1053 AN XY: 695756

African (AFR) AF: 0.0572 AC: 1846 AN: 32246

American (AMR) AF: 0.00486 AC: 217 AN: 44624

Ashkenazi Jewish (ASJ) AF: 0.000933 AC: 24 AN: 25712

East Asian (EAS) AF: 0.00 AC: 0 AN: 39246

South Asian (SAS) AF: 0.000283 AC: 24 AN: 84722

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53284

Middle Eastern (MID) AF: 0.00337 AC: 19 AN: 5632

European-Non Finnish (NFE) AF: 0.0000899 AC: 94 AN: 1045980

Other (OTH) AF: 0.00387 AC: 224 AN: 57884

GnomAD4 genome AF: 0.0172 AC: 2624 AN: 152312 Hom.: 74 Cov.: 33 AF XY: 0.0173 AC XY: 1292 AN XY: 74478

African (AFR) AF: 0.0589 AC: 2448 AN: 41562

American (AMR) AF: 0.00817 AC: 125 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10620

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000294 AC: 20 AN: 68032

Other (OTH) AF: 0.0128 AC: 27 AN: 2110

Alfa AF: 0.00833 Hom.: 11

Bravo AF: 0.0203

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.3
DANN	Benign	0.70
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3211891; hg19: chr7-80290348;