7-80602188-G-C

Variant summary

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

The ENST00000309881.11(CD36):​c.-375G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,940 control chromosomes in the GnomAD database, including 22,221 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 22221 hom., cov: 32)
Exomes 𝑓: 0.39 ( 0 hom. )

Consequence

CD36
ENST00000309881.11 5_prime_UTR

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -0.0130
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]

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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=-0.94).
BP6
Variant 7-80602188-G-C is Benign according to our data. Variant chr7-80602188-G-C is described in ClinVar as [Benign]. Clinvar id is 360740.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CD36NM_001001547.3 linkuse as main transcript upstream_gene_variant NP_001001547.1
CD36NM_001289911.2 linkuse as main transcript upstream_gene_variant NP_001276840.1
CD36NM_001371074.1 linkuse as main transcript upstream_gene_variant NP_001358003.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CD36ENST00000309881.11 linkuse as main transcriptc.-375G>C 5_prime_UTR_variant 1/141 ENSP00000308165 P1P16671-1
CD36ENST00000435819.5 linkuse as main transcriptc.-183-43900G>C intron_variant 2 ENSP00000399421 P1P16671-1
CD36ENST00000480599.6 linkuse as main transcriptn.39G>C non_coding_transcript_exon_variant 1/32

Frequencies

GnomAD3 genomes
AF:
0.528
AC:
80118
AN:
151804
Hom.:
22183
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.680
Gnomad AMI
AF:
0.493
Gnomad AMR
AF:
0.438
Gnomad ASJ
AF:
0.449
Gnomad EAS
AF:
0.682
Gnomad SAS
AF:
0.711
Gnomad FIN
AF:
0.463
Gnomad MID
AF:
0.497
Gnomad NFE
AF:
0.446
Gnomad OTH
AF:
0.495
GnomAD4 exome
AF:
0.389
AC:
7
AN:
18
Hom.:
0
Cov.:
0
AF XY:
0.333
AC XY:
4
AN XY:
12
show subpopulations
Gnomad4 NFE exome
AF:
0.375
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.528
AC:
80205
AN:
151922
Hom.:
22221
Cov.:
32
AF XY:
0.531
AC XY:
39426
AN XY:
74240
show subpopulations
Gnomad4 AFR
AF:
0.680
Gnomad4 AMR
AF:
0.438
Gnomad4 ASJ
AF:
0.449
Gnomad4 EAS
AF:
0.681
Gnomad4 SAS
AF:
0.711
Gnomad4 FIN
AF:
0.463
Gnomad4 NFE
AF:
0.446
Gnomad4 OTH
AF:
0.500
Alfa
AF:
0.467
Hom.:
9643
Bravo
AF:
0.525
Asia WGS
AF:
0.711
AC:
2470
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Platelet-type bleeding disorder 10 Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
4.1
DANN
Benign
0.64

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.

Other links and lift over

dbSNP: rs1194182; hg19: chr7-80231504; API