7-80650402-C-T

Variant names:

• chr7-80650402-C-T
• rs3211830
• NM_001001548.3:c.120+3542C>T

Variant summary

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

The NM_001001548.3(CD36):​c.120+3542C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0999 in 151,812 control chromosomes in the GnomAD database, including 1,057 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 0.10 (1057 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.120+3542C>T		intron_variant	Intron 3 of 14	ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.120+3542C>T		intron_variant	Intron 3 of 14	5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15170 AN: 151696 Hom.: 1060 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0978

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.0449

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0995

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0999 AC: 15171 AN: 151812 Hom.: 1057 Cov.: 32 AF XY: 0.102 AC XY: 7582 AN XY: 74218

African (AFR) AF: 0.117 AC: 4848 AN: 41430

American (AMR) AF: 0.0975 AC: 1487 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0695 AC: 240 AN: 3452

East Asian (EAS) AF: 0.329 AC: 1691 AN: 5146

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4816

European-Finnish (FIN) AF: 0.0673 AC: 711 AN: 10558

Middle Eastern (MID) AF: 0.0486 AC: 14 AN: 288

European-Non Finnish (NFE) AF: 0.0708 AC: 4804 AN: 67876

Other (OTH) AF: 0.0985 AC: 206 AN: 2092

Alfa AF: 0.0765 Hom.: 669

Bravo AF: 0.0973

Asia WGS AF: 0.280 AC: 970 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		-0.24
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: rs3211830; hg19: chr7-80279718;