Variant rs3211956 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.1419+299T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 334,970 control chromosomes in the GnomAD database, including 1,462 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.070 ( 532 hom., cov: 32)

Exomes 𝑓: 0.090 ( 930 hom. )

Consequence

CD36
NM_001001548.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.11

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=-0.83).

BP6

Variant 7-80674446-T-G is Benign according to our data. Variant chr7-80674446-T-G is described in ClinVar as [Benign]. Clinvar id is 1240468.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD36	NM_001001548.3 link	c.1419+299T>G		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.1419+299T>G		intron_variant		5	NM_001001548.3	ENSP00000415743.2		P16671-1

Frequencies

GnomAD3 genomes

AF:

0.0705

AC:

10719

AN:

151944

Hom.:

533

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0280

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0818

Gnomad ASJ

AF:

0.0792

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.0607

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0791

Gnomad OTH

AF:

0.0751

GnomAD4 exome

AF:

0.0899

AC:

16449

AN:

182908

Hom.:

930

Cov.:

AF XY:

0.0930

AC XY:

9209

AN XY:

99064

show subpopulations

Gnomad4 AFR exome

AF:

0.0266

Gnomad4 AMR exome

AF:

0.0801

Gnomad4 ASJ exome

AF:

0.0829

Gnomad4 EAS exome

AF:

0.245

Gnomad4 SAS exome

AF:

0.109

Gnomad4 FIN exome

AF:

0.0676

Gnomad4 NFE exome

AF:

0.0791

Gnomad4 OTH exome

AF:

0.0882

GnomAD4 genome

AF:

0.0705

AC:

10718

AN:

152062

Hom.:

532

Cov.:

AF XY:

0.0711

AC XY:

5282

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.0279

Gnomad4 AMR

AF:

0.0818

Gnomad4 ASJ

AF:

0.0792

Gnomad4 EAS

AF:

0.250

Gnomad4 SAS

AF:

0.113

Gnomad4 FIN

AF:

0.0607

Gnomad4 NFE

AF:

0.0791

Gnomad4 OTH

AF:

0.0753

Alfa

AF:

0.0776

Hom.:

482

Bravo

AF:

0.0667

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.13

DANN

Benign

0.80

Splicing

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