7-80660086-C-T

Variant names:

• chr7-80660086-C-T
• rs3211885
• NM_001001548.3:c.282-977C>T

Variant summary

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

The NM_000072.3(CD36):​c.282-977C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,910 control chromosomes in the GnomAD database, including 13,836 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 0.42 (13836 hom., cov: 32)
• Consequence: CD36 NM_000072.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.880
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000072.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001548.3	MANE Select	c.282-977C>T		intron	N/A	NP_001001548.1
	CD36	NM_000072.3		c.282-977C>T		intron	N/A	NP_000063.2
	CD36	NM_001001547.3		c.282-977C>T		intron	N/A	NP_001001547.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.282-977C>T		intron	N/A	ENSP00000415743.2
	CD36	ENST00000309881.11	TSL:1	c.282-977C>T		intron	N/A	ENSP00000308165.7
	CD36	ENST00000394788.7	TSL:1	c.282-977C>T		intron	N/A	ENSP00000378268.3

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64036 AN: 151792 Hom.: 13831 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.422 AC: 64069 AN: 151910 Hom.: 13836 Cov.: 32 AF XY: 0.426 AC XY: 31596 AN XY: 74208

African (AFR) AF: 0.385 AC: 15929 AN: 41420

American (AMR) AF: 0.395 AC: 6025 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1353 AN: 3464

East Asian (EAS) AF: 0.517 AC: 2670 AN: 5166

South Asian (SAS) AF: 0.678 AC: 3263 AN: 4814

European-Finnish (FIN) AF: 0.442 AC: 4653 AN: 10526

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28712 AN: 67946

Other (OTH) AF: 0.421 AC: 890 AN: 2114

Alfa AF: 0.415 Hom.: 16519

Bravo AF: 0.407

Asia WGS AF: 0.613 AC: 2126 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.23
PhyloP100		0.88
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: rs3211885; hg19: chr7-80289402;