rs1761667

chr7-80615623-G-A

Variant summary

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

The ENST00000309881.11(CD36):c.-184+13244G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,986 control chromosomes in the GnomAD database, including 18,385 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (18385 hom., cov: 32)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.10

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=-0.91).
• BP6: Variant 7-80615623-G-A is Benign according to our data. Variant chr7-80615623-G-A is described in ClinVar as [Benign]. Clinvar id is 487078.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001547.3	c.-184+13244G>A		intron_variant
CD36	NM_001289911.2	c.-109+13244G>A		intron_variant
CD36	NM_001371074.1	c.-180+13244G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000309881.11	c.-184+13244G>A		intron_variant		1		P1
CD36	ENST00000435819.5	c.-183-30465G>A		intron_variant		2		P1
CD36	ENST00000534394.5	c.-109+13244G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73410 AN: 151868 Hom.: 18377 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.483 AC: 73443 AN: 151986 Hom.: 18385 Cov.: 32 AF XY: 0.480 AC XY: 35654 AN XY: 74286

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.500

Alfa AF: 0.519 Hom.: 2581

Bravo AF: 0.489

Asia WGS AF: 0.291 AC: 1016 AN: 3478

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	-0.91
Cadd	Benign	0.53
Dann	Benign	0.75

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: rs1761667; hg19: chr7-80244939;