chr7-80624067-T-C

Position:

• chr7-80624067-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000309881.11(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 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001547.3	c.-184+21688T>C		intron_variant
CD36	NM_001289911.2	c.-109+21688T>C		intron_variant
CD36	NM_001371074.1	c.-180+21688T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000309881.11	c.-184+21688T>C		intron_variant		1		P1
CD36	ENST00000435819.5	c.-183-22021T>C		intron_variant		2		P1
CD36	ENST00000534394.5	c.-109+21688T>C		intron_variant		2

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

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

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.350

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	15
DANN	Benign	0.63

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: rs2151916; hg19: chr7-80253383;