Variant rs1527483 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001001548.3(CD36):c.1125+144G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0805 in 668,342 control chromosomes in the GnomAD database, including 2,846 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.070 ( 520 hom., cov: 32)

Exomes 𝑓: 0.084 ( 2326 hom. )

Consequence

CD36
NM_001001548.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.784

Variant links:

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]

CD36 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 7-80672184-G-A is Benign according to our data. Variant chr7-80672184-G-A is described in ClinVar as [Benign]. Clinvar id is 487079.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD36	NM_001001548.3 link	c.1125+144G>A		intron_variant		ENST00000447544.7	NP_001001548.1	P16671-1A4D1B1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7 link	c.1125+144G>A		intron_variant		5	NM_001001548.3	ENSP00000415743.2		P16671-1

Frequencies

GnomAD3 genomes

AF:

0.0698

AC:

10575

AN:

151396

Hom.:

521

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0278

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0808

Gnomad ASJ

AF:

0.0786

Gnomad EAS

AF:

0.248

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.0608

Gnomad MID

AF:

0.0548

Gnomad NFE

AF:

0.0782

Gnomad OTH

AF:

0.0749

GnomAD4 exome

AF:

0.0836

AC:

43224

AN:

516826

Hom.:

2326

AF XY:

0.0851

AC XY:

23485

AN XY:

275846

show subpopulations

Gnomad4 AFR exome

AF:

0.0262

Gnomad4 AMR exome

AF:

0.0729

Gnomad4 ASJ exome

AF:

0.0791

Gnomad4 EAS exome

AF:

0.228

Gnomad4 SAS exome

AF:

0.101

Gnomad4 FIN exome

AF:

0.0661

Gnomad4 NFE exome

AF:

0.0737

Gnomad4 OTH exome

AF:

0.0832

GnomAD4 genome

AF:

0.0698

AC:

10573

AN:

151516

Hom.:

520

Cov.:

AF XY:

0.0703

AC XY:

5205

AN XY:

74020

show subpopulations

Gnomad4 AFR

AF:

0.0278

Gnomad4 AMR

AF:

0.0807

Gnomad4 ASJ

AF:

0.0786

Gnomad4 EAS

AF:

0.248

Gnomad4 SAS

AF:

0.111

Gnomad4 FIN

AF:

0.0608

Gnomad4 NFE

AF:

0.0782

Gnomad4 OTH

AF:

0.0745

Alfa

AF:

0.0731

Hom.:

Bravo

AF:

0.0657

Asia WGS

AF:

0.174

AC:

599

AN:

3454

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

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

-0.86

CADD

Benign

0.33

DANN

Benign

0.59

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over