7-80520702-T-C

Variant names:

• chr7-80520702-T-C
• rs1107657
• ENST00000435819.5:c.-260-25489T>C

Variant summary

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

The ENST00000435819.5(CD36):​c.-260-25489T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,090 control chromosomes in the GnomAD database, including 38,141 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 0.70 (38141 hom., cov: 31)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900
• Publications: 3 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000435819.5	c.-260-25489T>C		intron_variant	Intron 3 of 16	2		ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106526 AN: 151972 Hom.: 38083 Cov.: 31

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.701 AC: 106631 AN: 152090 Hom.: 38141 Cov.: 31 AF XY: 0.703 AC XY: 52252 AN XY: 74350

African (AFR) AF: 0.848 AC: 35180 AN: 41506

American (AMR) AF: 0.674 AC: 10307 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2109 AN: 3470

East Asian (EAS) AF: 0.747 AC: 3853 AN: 5156

South Asian (SAS) AF: 0.556 AC: 2679 AN: 4816

European-Finnish (FIN) AF: 0.711 AC: 7512 AN: 10566

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42881 AN: 67978

Other (OTH) AF: 0.646 AC: 1365 AN: 2112

Alfa AF: 0.675 Hom.: 4334

Bravo AF: 0.707

Asia WGS AF: 0.644 AC: 2240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.56
PhyloP100		-0.90
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: rs1107657; hg19: chr7-80150018;