7-80650519-A-T

Variant names:

• chr7-80650519-A-T
• rs997906
• NM_001001548.3:c.120+3659A>T

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+3659A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,932 control chromosomes in the GnomAD database, including 7,498 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 0.30 (7498 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• 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: 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 = 0.425 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.120+3659A>T		intron	N/A	NP_001001548.1	P16671-1
	CD36	NM_000072.3		c.120+3659A>T		intron	N/A	NP_000063.2	A4D1B1
	CD36	NM_001001547.3		c.120+3659A>T		intron	N/A	NP_001001547.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.120+3659A>T		intron	N/A	ENSP00000415743.2	P16671-1
	CD36	ENST00000309881.11	TSL:1	c.120+3659A>T		intron	N/A	ENSP00000308165.7	P16671-1
	CD36	ENST00000394788.7	TSL:1	c.120+3659A>T		intron	N/A	ENSP00000378268.3	P16671-1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45518 AN: 151814 Hom.: 7502 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.300 AC: 45523 AN: 151932 Hom.: 7498 Cov.: 32 AF XY: 0.303 AC XY: 22482 AN XY: 74248

African (AFR) AF: 0.167 AC: 6934 AN: 41486

American (AMR) AF: 0.293 AC: 4473 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1179 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1240 AN: 5172

South Asian (SAS) AF: 0.441 AC: 2127 AN: 4822

European-Finnish (FIN) AF: 0.383 AC: 4028 AN: 10524

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24343 AN: 67888

Other (OTH) AF: 0.310 AC: 653 AN: 2108

Alfa AF: 0.200 Hom.: 471

Bravo AF: 0.284

Asia WGS AF: 0.332 AC: 1151 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.84
PhyloP100		0.039
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: rs997906; hg19: chr7-80279835;