NM_001001548.3:c.1419+609A>G

Variant names:

• chr7-80674756-A-G
• rs3211958
• NM_001001548.3:c.1419+609A>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.1419+609A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,876 control chromosomes in the GnomAD database, including 10,773 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 0.36 (10773 hom., cov: 31)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 16 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.1419+609A>G		intron_variant	Intron 14 of 14	ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.1419+609A>G		intron_variant	Intron 14 of 14	5	NM_001001548.3	ENSP00000415743.2
CD36	ENST00000464213.1	n.3285+609A>G		intron_variant	Intron 4 of 4	1
CD36	ENST00000488048.1	c.198+609A>G		intron_variant	Intron 2 of 2	3		ENSP00000435698.1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54403 AN: 151758 Hom.: 10768 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.358 AC: 54405 AN: 151876 Hom.: 10773 Cov.: 31 AF XY: 0.359 AC XY: 26612 AN XY: 74218

African (AFR) AF: 0.172 AC: 7134 AN: 41490

American (AMR) AF: 0.342 AC: 5205 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1515 AN: 3464

East Asian (EAS) AF: 0.441 AC: 2274 AN: 5156

South Asian (SAS) AF: 0.448 AC: 2156 AN: 4814

European-Finnish (FIN) AF: 0.446 AC: 4707 AN: 10562

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30081 AN: 67838

Other (OTH) AF: 0.384 AC: 810 AN: 2112

Alfa AF: 0.415 Hom.: 15407

Bravo AF: 0.340

Asia WGS AF: 0.456 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.48
PhyloP100		-0.92
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: rs3211958; hg19: chr7-80304072;