rs3212018

Positions:

• chr7-80674384-AGCACAAATAAAGCACT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000072.3(CD36):​c.*238_*253delGCACAAATAAAGCACT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 454,058 control chromosomes in the GnomAD database, including 4,110 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (1177 hom., cov: 30)
  • Exomes 𝑓: 0.14 (2933 hom.)
• Consequence: CD36 NM_000072.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.08

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 7-80674384-AGCACAAATAAAGCACT-A is Benign according to our data. Variant chr7-80674384-AGCACAAATAAAGCACT-A is described in ClinVar as [Benign]. Clinvar id is 1278201.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD36	NM_001001548.3	c.1419+238_1419+253delGCACAAATAAAGCACT		intron_variant		ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.1419+238_1419+253delGCACAAATAAAGCACT		intron_variant		5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17388 AN: 151890 Hom.: 1174 Cov.: 30

Gnomad AFR AF: 0.0542

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0730

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.119

GnomAD4 exome AF: 0.135 AC: 40867 AN: 302050 Hom.: 2933 AF XY: 0.135 AC XY: 21831 AN XY: 161886

Gnomad4 AFR exome AF: 0.0572

Gnomad4 AMR exome AF: 0.105

Gnomad4 ASJ exome AF: 0.159

Gnomad4 EAS exome AF: 0.0721

Gnomad4 SAS exome AF: 0.123

Gnomad4 FIN exome AF: 0.216

Gnomad4 NFE exome AF: 0.143

Gnomad4 OTH exome AF: 0.128

GnomAD4 genome AF: 0.114 AC: 17393 AN: 152008 Hom.: 1177 Cov.: 30 AF XY: 0.115 AC XY: 8558 AN XY: 74300

Gnomad4 AFR AF: 0.0540

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.0732

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.117

Alfa AF: 0.138 Hom.: 209

Bravo AF: 0.106

Asia WGS AF: 0.0790 AC: 276 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3212018; hg19: chr7-80303700; COSMIC: COSV59212855; COSMIC: COSV59212855;