chr7-80405632-A-G

Position:

• chr7-80405632-A-G

Variant summary

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

The ENST00000435819.5(CD36):​c.-478+35851A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,070 control chromosomes in the GnomAD database, including 1,531 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 0.12 (1531 hom., cov: 32)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000435819.5	c.-478+35851A>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18715 AN: 151952 Hom.: 1524 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0784

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0534

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0813

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.123 AC: 18748 AN: 152070 Hom.: 1531 Cov.: 32 AF XY: 0.120 AC XY: 8956 AN XY: 74364

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0783

Gnomad4 ASJ AF: 0.0878

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0534

Gnomad4 NFE AF: 0.0813

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0947 Hom.: 406

Bravo AF: 0.128

Asia WGS AF: 0.153 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.57

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: rs513740; hg19: chr7-80034948;