chr7-80624595-T-C

Variant names:

• chr7-80624595-T-C
• rs1537593
• ENST00000309881.11:c.-183-21493T>C

Variant summary

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

The ENST00000309881.11(CD36):​c.-183-21493T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 151,906 control chromosomes in the GnomAD database, including 50,417 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 0.80 (50417 hom., cov: 30)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001547.3	c.-183-21493T>C		intron_variant	Intron 1 of 13		NP_001001547.1
CD36	NM_001371074.1	c.-179-21497T>C		intron_variant	Intron 1 of 13		NP_001358003.1
CD36	NM_001371075.1	c.-183-21493T>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.-183-21493T>C		intron_variant	Intron 1 of 13	1		ENSP00000308165.7
CD36	ENST00000435819.5	c.-183-21493T>C		intron_variant	Intron 4 of 16	2		ENSP00000399421.1
CD36	ENST00000534394.5	c.-109+22216T>C		intron_variant	Intron 1 of 11	2		ENSP00000431296.1

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121941 AN: 151788 Hom.: 50412 Cov.: 30

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.803 AC: 121989 AN: 151906 Hom.: 50417 Cov.: 30 AF XY: 0.802 AC XY: 59555 AN XY: 74222

African (AFR) AF: 0.623 AC: 25765 AN: 41372

American (AMR) AF: 0.822 AC: 12534 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3106 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2843 AN: 5104

South Asian (SAS) AF: 0.736 AC: 3539 AN: 4806

European-Finnish (FIN) AF: 0.914 AC: 9696 AN: 10606

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61597 AN: 67986

Other (OTH) AF: 0.829 AC: 1748 AN: 2108

Alfa AF: 0.883 Hom.: 52069

Bravo AF: 0.793

Asia WGS AF: 0.629 AC: 2190 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.44
DANN	Benign	0.37
PhyloP100		-1.3
PromoterAI		0.0018	Neutral
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: rs1537593; hg19: chr7-80253911;