rs1334513

Variant names:

• chr7-80638639-C-A
• rs1334513
• ENST00000309881.11:c.-183-7449C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-80638639-C-A
• chr7-80638639-C-G
• chr7-80638639-C-T

Variant summary

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

The ENST00000309881.11(CD36):​c.-183-7449C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 151,226 control chromosomes in the GnomAD database, including 69,858 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 0.96 (69855 hom., cov: 27)
  • Exomes 𝑓: 1.0 (3 hom.)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821
• Publications: 5 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=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.-291C>A		upstream_gene_variant		ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.-291C>A		upstream_gene_variant		5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.961 AC: 145179 AN: 151104 Hom.: 69813 Cov.: 27

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.969

GnomAD4 exome AF: 1.00 AC: 6 AN: 6 Hom.: 3 Cov.: 0 AF XY: 1.00 AC XY: 4 AN XY: 4

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.961 AC: 145276 AN: 151220 Hom.: 69855 Cov.: 27 AF XY: 0.962 AC XY: 70991 AN XY: 73806

African (AFR) AF: 0.914 AC: 37643 AN: 41190

American (AMR) AF: 0.971 AC: 14695 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.964 AC: 3339 AN: 3462

East Asian (EAS) AF: 1.00 AC: 5095 AN: 5096

South Asian (SAS) AF: 0.996 AC: 4780 AN: 4800

European-Finnish (FIN) AF: 0.981 AC: 10203 AN: 10398

Middle Eastern (MID) AF: 0.979 AC: 286 AN: 292

European-Non Finnish (NFE) AF: 0.977 AC: 66298 AN: 67848

Other (OTH) AF: 0.969 AC: 2031 AN: 2096

Alfa AF: 0.968 Hom.: 26975

Bravo AF: 0.958

Asia WGS AF: 0.985 AC: 3426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.68
PhyloP100		0.82
PromoterAI		0.0076	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: rs1334513; hg19: chr7-80267955;