rs1334511

Variant names:

• chr7-80636752-A-G
• rs1334511
• ENST00000309881.11:c.-183-9336A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000309881.11(CD36):​c.-183-9336A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 151,972 control chromosomes in the GnomAD database, including 2,040 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.14 (2040 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 7 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001547.3	c.-183-9336A>G		intron_variant	Intron 1 of 13		NP_001001547.1
CD36	NM_001371074.1	c.-179-9340A>G		intron_variant	Intron 1 of 13		NP_001358003.1
CD36	NM_001371075.1	c.-183-9336A>G		intron_variant	Intron 1 of 14		NP_001358004.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000309881.11	c.-183-9336A>G		intron_variant	Intron 1 of 13	1		ENSP00000308165.7
CD36	ENST00000435819.5	c.-183-9336A>G		intron_variant	Intron 4 of 16	2		ENSP00000399421.1
CD36	ENST00000534394.5	c.-108-19788A>G		intron_variant	Intron 1 of 11	2		ENSP00000431296.1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20502 AN: 151854 Hom.: 2038 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0667

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.118

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

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: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.135 AC: 20528 AN: 151972 Hom.: 2040 Cov.: 32 AF XY: 0.136 AC XY: 10114 AN XY: 74304

African (AFR) AF: 0.238 AC: 9877 AN: 41434

American (AMR) AF: 0.108 AC: 1649 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1753 AN: 5152

South Asian (SAS) AF: 0.242 AC: 1165 AN: 4818

European-Finnish (FIN) AF: 0.0667 AC: 706 AN: 10586

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0711 AC: 4832 AN: 67960

Other (OTH) AF: 0.118 AC: 248 AN: 2106

Alfa AF: 0.0885 Hom.: 1104

Bravo AF: 0.137

Asia WGS AF: 0.295 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.77
PhyloP100		0.40
Mutation Taster		=100/0	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: rs1334511; hg19: chr7-80266068;