chr7-80624139-T-A

Variant names:

• chr7-80624139-T-A
• rs2366855
• ENST00000309881.11:c.-184+21760T>A

Variant summary

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

The NM_001371077.1(CD36):​c.-235T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,054 control chromosomes in the GnomAD database, including 16,727 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 0.45 (16726 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: CD36 NM_001371077.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 9 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001371077.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001371077.1		c.-235T>A		5_prime_UTR	Exon 1 of 15	NP_001358006.1
	CD36	NM_001371078.1		c.-235T>A		5_prime_UTR	Exon 1 of 14	NP_001358007.1
	CD36	NM_001001547.3		c.-184+21760T>A		intron	N/A	NP_001001547.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000309881.11	TSL:1	c.-184+21760T>A		intron	N/A	ENSP00000308165.7
	CD36	ENST00000855942.1		c.-231T>A		5_prime_UTR	Exon 1 of 15	ENSP00000526001.1
	CD36	ENST00000855945.1		c.-231T>A		5_prime_UTR	Exon 1 of 14	ENSP00000526004.1

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69088 AN: 151932 Hom.: 16724 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.484

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

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: 0.750 AC: 3 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.455 AC: 69110 AN: 152050 Hom.: 16726 Cov.: 32 AF XY: 0.452 AC XY: 33583 AN XY: 74344

African (AFR) AF: 0.300 AC: 12462 AN: 41500

American (AMR) AF: 0.508 AC: 7749 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1892 AN: 3466

East Asian (EAS) AF: 0.315 AC: 1629 AN: 5166

South Asian (SAS) AF: 0.289 AC: 1394 AN: 4826

European-Finnish (FIN) AF: 0.530 AC: 5606 AN: 10576

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.541 AC: 36758 AN: 67950

Other (OTH) AF: 0.479 AC: 1007 AN: 2102

Alfa AF: 0.390 Hom.: 1189

Bravo AF: 0.453

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		-0.83
PromoterAI		-0.013	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: rs2366855; hg19: chr7-80253455;