rs3173804

Variant names:

• chr7-80670534-T-A
• rs3173804
• ENST00000464213.1:n.1158T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-80670534-T-A
• chr7-80670534-T-C
• chr7-80670534-T-G

Variant summary

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

The ENST00000464213.1(CD36):​n.1158T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 211,616 control chromosomes in the GnomAD database, including 16,919 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 0.38 (11574 hom., cov: 32)
  • Exomes 𝑓: 0.41 (5345 hom.)
• Consequence: CD36 ENST00000464213.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685
• Publications: 12 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.819-443T>A		intron_variant	Intron 9 of 14	ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.819-443T>A		intron_variant	Intron 9 of 14	5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57919 AN: 151894 Hom.: 11567 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.392

GnomAD4 exome AF: 0.411 AC: 24489 AN: 59604 Hom.: 5345 Cov.: 0 AF XY: 0.413 AC XY: 12856 AN XY: 31092

African (AFR) AF: 0.211 AC: 252 AN: 1192

American (AMR) AF: 0.345 AC: 1293 AN: 3746

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 557 AN: 1280

East Asian (EAS) AF: 0.418 AC: 1329 AN: 3176

South Asian (SAS) AF: 0.424 AC: 3431 AN: 8086

European-Finnish (FIN) AF: 0.411 AC: 968 AN: 2356

Middle Eastern (MID) AF: 0.447 AC: 84 AN: 188

European-Non Finnish (NFE) AF: 0.419 AC: 15312 AN: 36568

Other (OTH) AF: 0.419 AC: 1263 AN: 3012

GnomAD4 genome AF: 0.381 AC: 57940 AN: 152012 Hom.: 11574 Cov.: 32 AF XY: 0.381 AC XY: 28317 AN XY: 74294

African (AFR) AF: 0.251 AC: 10416 AN: 41474

American (AMR) AF: 0.352 AC: 5382 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1503 AN: 3472

East Asian (EAS) AF: 0.436 AC: 2252 AN: 5160

South Asian (SAS) AF: 0.445 AC: 2145 AN: 4820

European-Finnish (FIN) AF: 0.446 AC: 4706 AN: 10550

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30182 AN: 67954

Other (OTH) AF: 0.397 AC: 839 AN: 2114

Alfa AF: 0.310 Hom.: 945

Bravo AF: 0.367

Asia WGS AF: 0.457 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.65
PhyloP100		0.69
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: rs3173804; hg19: chr7-80299850;