7-80675296-A-G

Variant names:

• chr7-80675296-A-G
• rs3211960
• NM_001001548.3:c.*1-1088A>G

Variant summary

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

The NM_001001548.3(CD36):​c.*1-1088A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,562 control chromosomes in the GnomAD database, including 10,569 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 0.35 (10569 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 4 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: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001548.3	MANE Select	c.*1-1088A>G		intron	N/A	NP_001001548.1	P16671-1
	CD36	NM_001371075.1		c.*1-1088A>G		intron	N/A	NP_001358004.1	P16671-1
	CD36	NM_001371077.1		c.*1-1088A>G		intron	N/A	NP_001358006.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.*1-1088A>G		intron	N/A	ENSP00000415743.2	P16671-1
	CD36	ENST00000464213.1	TSL:1	n.3286-1088A>G		intron	N/A
	CD36	ENST00000855930.1		c.*1149A>G		3_prime_UTR	Exon 14 of 14	ENSP00000525989.1

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53144 AN: 151446 Hom.: 10564 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.351 AC: 53142 AN: 151562 Hom.: 10569 Cov.: 32 AF XY: 0.352 AC XY: 26062 AN XY: 74102

African (AFR) AF: 0.144 AC: 5894 AN: 41016

American (AMR) AF: 0.339 AC: 5170 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1518 AN: 3472

East Asian (EAS) AF: 0.439 AC: 2268 AN: 5166

South Asian (SAS) AF: 0.448 AC: 2164 AN: 4830

European-Finnish (FIN) AF: 0.445 AC: 4704 AN: 10576

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30119 AN: 67950

Other (OTH) AF: 0.375 AC: 791 AN: 2110

Alfa AF: 0.381 Hom.: 1756

Bravo AF: 0.331

Asia WGS AF: 0.452 AC: 1569 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.45
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3211960; hg19: chr7-80304612;