chr7-80524699-T-C

Variant names:

• chr7-80524699-T-C
• rs2012380
• ENST00000435819.5:c.-260-21492T>C

Variant summary

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

The ENST00000435819.5(CD36):​c.-260-21492T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,818 control chromosomes in the GnomAD database, including 36,073 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 0.68 (36073 hom., cov: 30)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 1 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

LOC124901685 (HGNC:):

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 = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901685	XR_007060402.1	n.-148T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000435819.5	c.-260-21492T>C		intron_variant	Intron 3 of 16	2		ENSP00000399421.1
CD36	ENST00000648416.1	n.-162T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102639 AN: 151700 Hom.: 36012 Cov.: 30

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.677 AC: 102759 AN: 151818 Hom.: 36073 Cov.: 30 AF XY: 0.677 AC XY: 50247 AN XY: 74198

African (AFR) AF: 0.862 AC: 35692 AN: 41430

American (AMR) AF: 0.662 AC: 10097 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3636 AN: 5132

South Asian (SAS) AF: 0.455 AC: 2190 AN: 4816

European-Finnish (FIN) AF: 0.678 AC: 7125 AN: 10506

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39943 AN: 67912

Other (OTH) AF: 0.635 AC: 1335 AN: 2104

Alfa AF: 0.524 Hom.: 1476

Bravo AF: 0.688

Asia WGS AF: 0.588 AC: 2047 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	1.6
DANN	Benign	0.22
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2012380; hg19: chr7-80154015;