7-80641126-A-G

Variant names:

• chr7-80641126-A-G
• rs4728191
• NM_001001548.3:c.-184+2380A>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.-184+2380A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.955 in 152,076 control chromosomes in the GnomAD database, including 69,525 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 0.96 (69525 hom., cov: 31)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• 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: 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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.-184+2380A>G		intron	N/A	NP_001001548.1
	CD36	NM_000072.3		c.-184+2380A>G		intron	N/A	NP_000063.2
	CD36	NM_001001547.3		c.-183-4962A>G		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.-184+2380A>G		intron	N/A	ENSP00000415743.2
	CD36	ENST00000309881.11	TSL:1	c.-183-4962A>G		intron	N/A	ENSP00000308165.7
	CD36	ENST00000394788.7	TSL:1	c.-184+2380A>G		intron	N/A	ENSP00000378268.3

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145195 AN: 151958 Hom.: 69486 Cov.: 31

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.973

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.966

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

GnomAD4 genome AF: 0.955 AC: 145291 AN: 152076 Hom.: 69525 Cov.: 31 AF XY: 0.957 AC XY: 71153 AN XY: 74348

African (AFR) AF: 0.894 AC: 37078 AN: 41478

American (AMR) AF: 0.973 AC: 14831 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3349 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5150 AN: 5150

South Asian (SAS) AF: 0.996 AC: 4805 AN: 4826

European-Finnish (FIN) AF: 0.981 AC: 10420 AN: 10618

Middle Eastern (MID) AF: 0.979 AC: 286 AN: 292

European-Non Finnish (NFE) AF: 0.977 AC: 66420 AN: 67968

Other (OTH) AF: 0.966 AC: 2044 AN: 2116

Alfa AF: 0.968 Hom.: 31216

Bravo AF: 0.953

Asia WGS AF: 0.982 AC: 3416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.64
PhyloP100		-0.38
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: rs4728191; hg19: chr7-80270442;