7-80604927-G-T

Position:

• chr7-80604927-G-T

Variant summary

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

The ENST00000309881.11(CD36):​c.-184+2548G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,740 control chromosomes in the GnomAD database, including 15,094 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 0.44 (15094 hom., cov: 31)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD36	NM_001001547.3	c.-184+2548G>T		intron_variant			NP_001001547.1
CD36	NM_001289911.2	c.-109+2548G>T		intron_variant			NP_001276840.1
CD36	NM_001371074.1	c.-180+2548G>T		intron_variant			NP_001358003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000309881.11	c.-184+2548G>T		intron_variant		1		ENSP00000308165	P1
CD36	ENST00000435819.5	c.-183-41161G>T		intron_variant		2		ENSP00000399421	P1
CD36	ENST00000534394.5	c.-109+2548G>T		intron_variant		2		ENSP00000431296

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66789 AN: 151622 Hom.: 15079 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.424

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.440 AC: 66838 AN: 151740 Hom.: 15094 Cov.: 31 AF XY: 0.445 AC XY: 33026 AN XY: 74148

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.430

Alfa AF: 0.419 Hom.: 15308

Bravo AF: 0.426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.14
DANN	Benign	0.78

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: rs17154155; hg19: chr7-80234243;