7-80520815-T-G

Variant names:

• chr7-80520815-T-G
• rs1107660
• ENST00000435819.5:c.-260-25376T>G

Variant summary

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

The ENST00000435819.5(CD36):​c.-260-25376T>G 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 151,928 control chromosomes in the GnomAD database, including 38,123 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 (38123 hom., cov: 30)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 7 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=-1.0).
• 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.-260-25376T>G		intron_variant	Intron 3 of 16	2		ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106420 AN: 151810 Hom.: 38065 Cov.: 30

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.701 AC: 106525 AN: 151928 Hom.: 38123 Cov.: 30 AF XY: 0.703 AC XY: 52138 AN XY: 74204

African (AFR) AF: 0.848 AC: 35162 AN: 41476

American (AMR) AF: 0.675 AC: 10293 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2109 AN: 3472

East Asian (EAS) AF: 0.748 AC: 3860 AN: 5160

South Asian (SAS) AF: 0.556 AC: 2663 AN: 4788

European-Finnish (FIN) AF: 0.711 AC: 7485 AN: 10534

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42848 AN: 67936

Other (OTH) AF: 0.646 AC: 1363 AN: 2110

Alfa AF: 0.651 Hom.: 144625

Bravo AF: 0.708

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	0.49
DANN	Benign	0.47
PhyloP100		-1.7
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: rs1107660; hg19: chr7-80150131;