7-80665985-T-C

Variant names:

• chr7-80665985-T-C
• rs3211917
• ENST00000464213.1:n.72T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000464213.1(CD36):​n.72T>C 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 0.0141 in 160,634 control chromosomes in the GnomAD database, including 65 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 0.015 (65 hom., cov: 32)
  • Exomes 𝑓: 0.00036 (0 hom.)
• Consequence: CD36 ENST00000464213.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 1 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=-0.81).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0148 (2258/152226) while in subpopulation AFR AF = 0.0515 (2139/41542). AF 95% confidence interval is 0.0497. There are 65 homozygotes in GnomAd4. There are 1056 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 65 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000464213.1. 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.702-458T>C		intron	N/A	NP_001001548.1
	CD36	NM_000072.3		c.702-458T>C		intron	N/A	NP_000063.2
	CD36	NM_001001547.3		c.702-458T>C		intron	N/A	NP_001001547.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000464213.1	TSL:1	n.72T>C		non_coding_transcript_exon	Exon 1 of 5
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.702-458T>C		intron	N/A	ENSP00000415743.2
	CD36	ENST00000309881.11	TSL:1	c.702-458T>C		intron	N/A	ENSP00000308165.7

Frequencies

GnomAD3 genomes AF: 0.0148 AC: 2248 AN: 152108 Hom.: 65 Cov.: 32

Gnomad AFR AF: 0.0514

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00399

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000250

Gnomad OTH AF: 0.00861

GnomAD4 exome AF: 0.000357 AC: 3 AN: 8408 Hom.: 0 Cov.: 0 AF XY: 0.000220 AC XY: 1 AN XY: 4544

African (AFR) AF: 0.0227 AC: 1 AN: 44

American (AMR) AF: 0.00 AC: 0 AN: 1128

Ashkenazi Jewish (ASJ) AF: 0.00833 AC: 1 AN: 120

East Asian (EAS) AF: 0.00 AC: 0 AN: 380

South Asian (SAS) AF: 0.00 AC: 0 AN: 844

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 224

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 22

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 5294

Other (OTH) AF: 0.00284 AC: 1 AN: 352

GnomAD4 genome AF: 0.0148 AC: 2258 AN: 152226 Hom.: 65 Cov.: 32 AF XY: 0.0142 AC XY: 1056 AN XY: 74438

African (AFR) AF: 0.0515 AC: 2139 AN: 41542

American (AMR) AF: 0.00399 AC: 61 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000250 AC: 17 AN: 67986

Other (OTH) AF: 0.00852 AC: 18 AN: 2112

Alfa AF: 0.0119 Hom.: 4

Bravo AF: 0.0171

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism

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: rs3211917; hg19: chr7-80295301;