7-80638588-G-T

Variant names:

• chr7-80638588-G-T
• rs1334512
• ENST00000309881.11:c.-183-7500G>T

Variant summary

Our verdict is Benign. The variant received -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
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 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.-342G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 14	NP_000063.2	A4D1B1
	CD36	NM_000072.3		c.-342G>T		5_prime_UTR	Exon 1 of 14	NP_000063.2	A4D1B1
	CD36	NM_001001547.3		c.-183-7500G>T		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.-183-7500G>T		intron	N/A	ENSP00000308165.7	P16671-1
	CD36	ENST00000855951.1		c.-338G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 15	ENSP00000526010.1
	CD36	ENST00000956951.1		c.-342G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 15	ENSP00000627010.1

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

African (AFR) AF: 0.500 AC: 1 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) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.255 AC: 9936 AN: 38970

American (AMR) AF: 0.301 AC: 4314 AN: 14340

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1130 AN: 3382

East Asian (EAS) AF: 0.239 AC: 1152 AN: 4818

South Asian (SAS) AF: 0.442 AC: 1919 AN: 4346

European-Finnish (FIN) AF: 0.379 AC: 3484 AN: 9196

Middle Eastern (MID) AF: 0.379 AC: 106 AN: 280

European-Non Finnish (NFE) AF: 0.360 AC: 23674 AN: 65842

Other (OTH) AF: 0.329 AC: 659 AN: 2002

Alfa AF: 0.301 Hom.: 2243

Bravo AF: 0.313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.40
PhyloP100		-0.25
PromoterAI		0.00080	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: rs1334512; hg19: chr7-80267904; COSMIC: COSV59209686; COSMIC: COSV59209686;