7-80622979-A-C

Variant names:

• chr7-80622979-A-C
• rs12706912
• ENST00000309881.11:c.-184+20600A>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 6 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 -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
CD36	NM_001001547.3	c.-184+20600A>C		intron_variant	Intron 1 of 13		NP_001001547.1
CD36	NM_001371074.1	c.-180+20600A>C		intron_variant	Intron 1 of 13		NP_001358003.1
CD36	NM_001371075.1	c.-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
CD36	ENST00000309881.11	c.-184+20600A>C		intron_variant	Intron 1 of 13	1		ENSP00000308165.7
CD36	ENST00000435819.5	c.-183-23109A>C		intron_variant	Intron 4 of 16	2		ENSP00000399421.1
CD36	ENST00000534394.5	c.-109+20600A>C		intron_variant	Intron 1 of 11	2		ENSP00000431296.1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 73470 AN: 150492 Hom.: 18265 Cov.: 30

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

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

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

Other links and lift over

dbSNP: rs12706912; hg19: chr7-80252295;