rs3212018

Variant names:

• chr7-80674384-AGCACAAATAAAGCACT-A
• rs3212018
• ENST00000309881.11:c.*238_*253delGCACAAATAAAGCACT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000309881.11(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. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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 ENST00000309881.11 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.08
• Publications: 16 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

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.1419+238_1419+253delGCACAAATAAAGCACT		intron_variant	Intron 14 of 14	ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.1419+238_1419+253delGCACAAATAAAGCACT		intron_variant	Intron 14 of 14	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

African (AFR) AF: 0.0572 AC: 526 AN: 9196

American (AMR) AF: 0.105 AC: 1179 AN: 11248

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 1448 AN: 9126

East Asian (EAS) AF: 0.0721 AC: 1333 AN: 18498

South Asian (SAS) AF: 0.123 AC: 4579 AN: 37122

European-Finnish (FIN) AF: 0.216 AC: 3210 AN: 14894

Middle Eastern (MID) AF: 0.0997 AC: 127 AN: 1274

European-Non Finnish (NFE) AF: 0.143 AC: 26269 AN: 183586

Other (OTH) AF: 0.128 AC: 2196 AN: 17106

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

African (AFR) AF: 0.0540 AC: 2244 AN: 41522

American (AMR) AF: 0.105 AC: 1608 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3470

East Asian (EAS) AF: 0.0732 AC: 378 AN: 5166

South Asian (SAS) AF: 0.121 AC: 586 AN: 4824

European-Finnish (FIN) AF: 0.206 AC: 2178 AN: 10574

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9483 AN: 67874

Other (OTH) AF: 0.117 AC: 248 AN: 2112

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

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

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