7-80624067-T-C

Variant names:

• chr7-80624067-T-C
• rs2151916
• ENST00000309881.11:c.-184+21688T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001001547.3(CD36):​c.-184+21688T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,000 control chromosomes in the GnomAD database, including 9,256 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 0.35 (9255 hom., cov: 32)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: CD36 NM_001001547.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 16 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001547.3. 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_001001547.3		c.-184+21688T>C		intron	N/A	NP_001001547.1	P16671-1
	CD36	NM_001371074.1		c.-180+21688T>C		intron	N/A	NP_001358003.1	P16671-1
	CD36	NM_001371075.1		c.-184+21688T>C		intron	N/A	NP_001358004.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000309881.11	TSL:1	c.-184+21688T>C		intron	N/A	ENSP00000308165.7	P16671-1
	CD36	ENST00000956936.1		c.-473T>C		5_prime_UTR_premature_start_codon_gain	Exon 2 of 16	ENSP00000626995.1
	CD36	ENST00000956936.1		c.-473T>C		5_prime_UTR	Exon 2 of 16	ENSP00000626995.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52695 AN: 151872 Hom.: 9257 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.345

GnomAD4 exome AF: 0.333 AC: 4 AN: 12 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 4 AN XY: 8

African (AFR) AF: 0.00 AC: 0 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: 0.750 AC: 3 AN: 4

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.347 AC: 52716 AN: 151988 Hom.: 9255 Cov.: 32 AF XY: 0.349 AC XY: 25900 AN XY: 74272

African (AFR) AF: 0.319 AC: 13211 AN: 41472

American (AMR) AF: 0.313 AC: 4780 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1199 AN: 3460

East Asian (EAS) AF: 0.240 AC: 1235 AN: 5156

South Asian (SAS) AF: 0.447 AC: 2147 AN: 4808

European-Finnish (FIN) AF: 0.385 AC: 4068 AN: 10570

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.365 AC: 24794 AN: 67958

Other (OTH) AF: 0.350 AC: 740 AN: 2112

Alfa AF: 0.191 Hom.: 357

Bravo AF: 0.338

Asia WGS AF: 0.347 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	15
DANN	Benign	0.63
PhyloP100		0.076
PromoterAI		0.0034	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: rs2151916; hg19: chr7-80253383;