Variant chr7-80664600-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.361

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 -20 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_multiple_submitters_no_conflicts, 2 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	Protein	UniProt
CD36	NM_001001548.3 linkuse as main transcript	c.701+103C>T		intron_variant		ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7 linkuse as main transcript	c.701+103C>T		intron_variant		5	NM_001001548.3	ENSP00000415743	P1	P16671-1

Frequencies

GnomAD3 genomes

AF:

0.0528

AC:

8028

AN:

152004

Hom.:

327

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.0539

AC XY:

4007

AN XY:

74360

show subpopulations

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:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

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

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