7-80648791-T-G

Variant names:

• chr7-80648791-T-G
• rs3211817
• NM_001001548.3:c.120+1931T>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.120+1931T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0975 in 152,018 control chromosomes in the GnomAD database, including 1,016 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 0.097 (1016 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 5 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=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 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.120+1931T>G		intron	N/A	NP_001001548.1
	CD36	NM_000072.3		c.120+1931T>G		intron	N/A	NP_000063.2
	CD36	NM_001001547.3		c.120+1931T>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.120+1931T>G		intron	N/A	ENSP00000415743.2
	CD36	ENST00000309881.11	TSL:1	c.120+1931T>G		intron	N/A	ENSP00000308165.7
	CD36	ENST00000394788.7	TSL:1	c.120+1931T>G		intron	N/A	ENSP00000378268.3

Frequencies

GnomAD3 genomes AF: 0.0976 AC: 14820 AN: 151902 Hom.: 1019 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0971

Gnomad ASJ AF: 0.0693

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.0668

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.0975 AC: 14821 AN: 152018 Hom.: 1016 Cov.: 32 AF XY: 0.0999 AC XY: 7425 AN XY: 74306

African (AFR) AF: 0.109 AC: 4518 AN: 41498

American (AMR) AF: 0.0968 AC: 1477 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0693 AC: 240 AN: 3464

East Asian (EAS) AF: 0.331 AC: 1700 AN: 5134

South Asian (SAS) AF: 0.239 AC: 1153 AN: 4820

European-Finnish (FIN) AF: 0.0668 AC: 708 AN: 10602

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0705 AC: 4790 AN: 67932

Other (OTH) AF: 0.0953 AC: 201 AN: 2110

Alfa AF: 0.0901 Hom.: 116

Bravo AF: 0.0952

Asia WGS AF: 0.282 AC: 980 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.88
PhyloP100		1.5
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: rs3211817; hg19: chr7-80278107;