rs3211867

Positions:

• chr7-80657624-C-A
• chr7-80657624-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001001548.3(CD36):​c.281+924C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 151,946 control chromosomes in the GnomAD database, including 2,362 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.15 (2362 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.742

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 7-80657624-C-A is Benign according to our data. Variant chr7-80657624-C-A is described in ClinVar as [Benign]. Clinvar id is 1697965.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001548.3	c.281+924C>A		intron_variant		ENST00000447544.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000447544.7	c.281+924C>A		intron_variant		5	NM_001001548.3	P1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22067 AN: 151828 Hom.: 2357 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0710

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.145 AC: 22098 AN: 151946 Hom.: 2362 Cov.: 32 AF XY: 0.147 AC XY: 10884 AN XY: 74264

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0701

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.0711

Gnomad4 OTH AF: 0.127

Alfa AF: 0.122 Hom.: 237

Bravo AF: 0.149

Asia WGS AF: 0.288 AC: 999 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Type 2 diabetes mellitus Benign:1

Benign, criteria provided, single submitter

case-control

Faculté de Médecine, de Pharmacie et d'odontostomatologie, Université Cheikh Anta Diop

Jul 21, 2022

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.35

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: rs3211867; hg19: chr7-80286940;