rs1194182

Variant names:

• chr7-80602188-G-C
• rs1194182
• ENST00000309881.11:c.-375G>C

Your query was ambiguous. Multiple possible variants found:

• chr7-80602188-G-C
• chr7-80602188-G-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0130
• Publications: 20 publications found

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 Gene-Disease associations (from GenCC):

• platelet-type bleeding disorder 10

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
CD36	NM_001001547.3	c.-375G>C		upstream_gene_variant			NP_001001547.1
CD36	NM_001371074.1	c.-371G>C		upstream_gene_variant			NP_001358003.1
CD36	NM_001371075.1	c.-375G>C		upstream_gene_variant			NP_001358004.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000309881.11	c.-375G>C		5_prime_UTR_variant	Exon 1 of 14	1		ENSP00000308165.7
CD36	ENST00000480599.6	n.39G>C		non_coding_transcript_exon_variant	Exon 1 of 3	2
CD36	ENST00000435819.5	c.-183-43900G>C		intron_variant	Intron 4 of 16	2		ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80118 AN: 151804 Hom.: 22183 Cov.: 32

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 6 AN: 16

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.528 AC: 80205 AN: 151922 Hom.: 22221 Cov.: 32 AF XY: 0.531 AC XY: 39426 AN XY: 74240

African (AFR) AF: 0.680 AC: 28209 AN: 41464

American (AMR) AF: 0.438 AC: 6680 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1557 AN: 3468

East Asian (EAS) AF: 0.681 AC: 3495 AN: 5130

South Asian (SAS) AF: 0.711 AC: 3425 AN: 4820

European-Finnish (FIN) AF: 0.463 AC: 4884 AN: 10554

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30308 AN: 67924

Other (OTH) AF: 0.500 AC: 1053 AN: 2106

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

Submissions by phenotype

Platelet-type bleeding disorder 10 Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This 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

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.64
PhyloP100		-0.013
PromoterAI		-0.0074	Neutral
Mutation Taster		=292/8	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1194182; hg19: chr7-80231504;