chr7-80654141-A-C

Variant names:

• chr7-80654141-A-C
• rs3211851
• NM_001001548.3:c.121-2399A>C

Variant summary

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

The NM_001001548.3(CD36):​c.121-2399A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,136 control chromosomes in the GnomAD database, including 1,752 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 0.13 (1752 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001548.3. 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.121-2399A>C		intron	N/A	NP_001001548.1
	CD36	NM_000072.3		c.121-2399A>C		intron	N/A	NP_000063.2
	CD36	NM_001001547.3		c.121-2399A>C		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.121-2399A>C		intron	N/A	ENSP00000415743.2
	CD36	ENST00000309881.11	TSL:1	c.121-2399A>C		intron	N/A	ENSP00000308165.7
	CD36	ENST00000394788.7	TSL:1	c.121-2399A>C		intron	N/A	ENSP00000378268.3

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19704 AN: 152018 Hom.: 1749 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0740

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.0694

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.130 AC: 19730 AN: 152136 Hom.: 1752 Cov.: 32 AF XY: 0.131 AC XY: 9753 AN XY: 74384

African (AFR) AF: 0.209 AC: 8660 AN: 41480

American (AMR) AF: 0.116 AC: 1773 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0740 AC: 257 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1664 AN: 5168

South Asian (SAS) AF: 0.237 AC: 1140 AN: 4820

European-Finnish (FIN) AF: 0.0694 AC: 736 AN: 10606

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0762 AC: 5183 AN: 67992

Other (OTH) AF: 0.125 AC: 263 AN: 2112

Alfa AF: 0.0574 Hom.: 69

Bravo AF: 0.131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.4
DANN	Benign	0.65
PhyloP100		0.14
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: rs3211851; hg19: chr7-80283457;