chr7-80638639-C-A

Variant names:

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

Variant summary

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

The NM_000072.3(CD36):​c.-291C>A variant causes a 5 prime UTR premature start codon gain 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 NM_000072.3 5_prime_UTR_premature_start_codon_gain
• 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: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000072.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_000072.3		c.-291C>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 14	NP_000063.2	A4D1B1
	CD36	NM_000072.3		c.-291C>A		5_prime_UTR	Exon 1 of 14	NP_000063.2	A4D1B1
	CD36	NM_001001547.3		c.-183-7449C>A		intron	N/A	NP_001001547.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000309881.11	TSL:1	c.-183-7449C>A		intron	N/A	ENSP00000308165.7	P16671-1
	CD36	ENST00000855951.1		c.-287C>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 15	ENSP00000526010.1
	CD36	ENST00000855958.1		c.-287C>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 14	ENSP00000526017.1

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 v4.9

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;