rs3211908

chr7-80664600-C-T

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.701+103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0632 in 759,756 control chromosomes in the GnomAD database, including 2,017 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.053 (327 hom., cov: 32)
  • Exomes 𝑓: 0.066 (1690 hom.)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.361

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=-0.81).
• BP6: Variant 7-80664600-C-T is Benign according to our data. Variant chr7-80664600-C-T is described in ClinVar as [Benign]. Clinvar id is 1259835.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001548.3	c.701+103C>T		intron_variant		ENST00000447544.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000447544.7	c.701+103C>T		intron_variant		5	NM_001001548.3	P1

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 8028 AN: 152004 Hom.: 327 Cov.: 32

Gnomad AFR AF: 0.0251

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.0934

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0513

Gnomad OTH AF: 0.0549

GnomAD4 exome AF: 0.0657 AC: 39947 AN: 607634 Hom.: 1690 AF XY: 0.0670 AC XY: 22096 AN XY: 329766

Gnomad4 AFR exome AF: 0.0254

Gnomad4 AMR exome AF: 0.0852

Gnomad4 ASJ exome AF: 0.0633

Gnomad4 EAS exome AF: 0.170

Gnomad4 SAS exome AF: 0.0892

Gnomad4 FIN exome AF: 0.0608

Gnomad4 NFE exome AF: 0.0519

Gnomad4 OTH exome AF: 0.0635

GnomAD4 genome AF: 0.0528 AC: 8032 AN: 152122 Hom.: 327 Cov.: 32 AF XY: 0.0539 AC XY: 4007 AN XY: 74360

Gnomad4 AFR AF: 0.0250

Gnomad4 AMR AF: 0.0773

Gnomad4 ASJ AF: 0.0580

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.0941

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.0513

Gnomad4 OTH AF: 0.0543

Alfa AF: 0.0516 Hom.: 251

Bravo AF: 0.0504

Asia WGS AF: 0.146 AC: 505 AN: 3476

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	-0.81
Cadd	Benign	0.54
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: rs3211908; hg19: chr7-80293916; COSMIC: COSV59215759; COSMIC: COSV59215759;