7-80638588-G-T

Position:

• chr7-80638588-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000072.3(CD36):​c.-342G>T 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 0.325 in 144,078 control chromosomes in the GnomAD database, including 7,750 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 0.32 (7750 hom., cov: 23)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: CD36 NM_000072.3 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD36	NM_000072.3	c.-342G>T		5_prime_UTR_premature_start_codon_gain_variant	1/14		NP_000063.2
CD36	XM_005250715.6	c.-342G>T		5_prime_UTR_premature_start_codon_gain_variant	1/15		XP_005250772.1
CD36	XM_024447002.2	c.-342G>T		5_prime_UTR_premature_start_codon_gain_variant	1/15		XP_024302770.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000309881.11	c.-183-7500G>T		intron_variant		1		ENSP00000308165.7
CD36	ENST00000433696	c.-342G>T		5_prime_UTR_premature_start_codon_gain_variant	1/12	5		ENSP00000401863.2
CD36	ENST00000538969	c.-342G>T		5_prime_UTR_premature_start_codon_gain_variant	1/13	5		ENSP00000439543.1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 46782 AN: 143970 Hom.: 7753 Cov.: 23

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.323

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.325 AC: 46793 AN: 144070 Hom.: 7750 Cov.: 23 AF XY: 0.326 AC XY: 22774 AN XY: 69884

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.329

Alfa AF: 0.262 Hom.: 1003

Bravo AF: 0.313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs1334512; hg19: chr7-80267904; COSMIC: COSV59209686; COSMIC: COSV59209686;