rs1405747

chr7-80672620-C-A

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.1126-150C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 622,158 control chromosomes in the GnomAD database, including 58,529 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.40 (12254 hom., cov: 33)
  • Exomes 𝑓: 0.44 (46275 hom.)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.388

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=-0.93).
• BP6: Variant 7-80672620-C-A is Benign according to our data. Variant chr7-80672620-C-A is described in ClinVar as [Benign]. Clinvar id is 1294701.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001548.3	c.1126-150C>A		intron_variant		ENST00000447544.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000447544.7	c.1126-150C>A		intron_variant		5	NM_001001548.3	P1

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60165 AN: 151336 Hom.: 12240 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.445

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.401

GnomAD4 exome AF: 0.439 AC: 206765 AN: 470700 Hom.: 46275 AF XY: 0.441 AC XY: 111179 AN XY: 251974

Gnomad4 AFR exome AF: 0.304

Gnomad4 AMR exome AF: 0.336

Gnomad4 ASJ exome AF: 0.417

Gnomad4 EAS exome AF: 0.557

Gnomad4 SAS exome AF: 0.449

Gnomad4 FIN exome AF: 0.445

Gnomad4 NFE exome AF: 0.440

Gnomad4 OTH exome AF: 0.440

GnomAD4 genome AF: 0.397 AC: 60204 AN: 151458 Hom.: 12254 Cov.: 33 AF XY: 0.398 AC XY: 29414 AN XY: 73974

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.406

Alfa AF: 0.426 Hom.: 2794

Bravo AF: 0.385

Asia WGS AF: 0.504 AC: 1743 AN: 3464

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.66
Dann	Benign	0.53

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: rs1405747; hg19: chr7-80301936;