chr7-80672184-G-A

Variant names:

• chr7-80672184-G-A
• rs1527483
• NM_001001548.3:c.1125+144G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001001548.3(CD36):​c.1125+144G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0805 in 668,342 control chromosomes in the GnomAD database, including 2,846 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.070 (520 hom., cov: 32)
  • Exomes 𝑓: 0.084 (2326 hom.)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.784
• Publications: 51 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 7-80672184-G-A is Benign according to our data. Variant chr7-80672184-G-A is described in ClinVar as Benign. ClinVar VariationId is 487079.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.1125+144G>A		intron_variant	Intron 11 of 14	ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.1125+144G>A		intron_variant	Intron 11 of 14	5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.0698 AC: 10575 AN: 151396 Hom.: 521 Cov.: 32

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.0548

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0749

GnomAD4 exome AF: 0.0836 AC: 43224 AN: 516826 Hom.: 2326 AF XY: 0.0851 AC XY: 23485 AN XY: 275846

African (AFR) AF: 0.0262 AC: 358 AN: 13646

American (AMR) AF: 0.0729 AC: 1627 AN: 22312

Ashkenazi Jewish (ASJ) AF: 0.0791 AC: 1206 AN: 15246

East Asian (EAS) AF: 0.228 AC: 6644 AN: 29086

South Asian (SAS) AF: 0.101 AC: 4640 AN: 46078

European-Finnish (FIN) AF: 0.0661 AC: 1850 AN: 27980

Middle Eastern (MID) AF: 0.0361 AC: 73 AN: 2022

European-Non Finnish (NFE) AF: 0.0737 AC: 24514 AN: 332680

Other (OTH) AF: 0.0832 AC: 2312 AN: 27776

GnomAD4 genome AF: 0.0698 AC: 10573 AN: 151516 Hom.: 520 Cov.: 32 AF XY: 0.0703 AC XY: 5205 AN XY: 74020

African (AFR) AF: 0.0278 AC: 1150 AN: 41426

American (AMR) AF: 0.0807 AC: 1229 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0786 AC: 272 AN: 3462

East Asian (EAS) AF: 0.248 AC: 1278 AN: 5156

South Asian (SAS) AF: 0.111 AC: 531 AN: 4796

European-Finnish (FIN) AF: 0.0608 AC: 639 AN: 10514

Middle Eastern (MID) AF: 0.0552 AC: 16 AN: 290

European-Non Finnish (NFE) AF: 0.0782 AC: 5291 AN: 67634

Other (OTH) AF: 0.0745 AC: 157 AN: 2106

Alfa AF: 0.0695 Hom.: 292

Bravo AF: 0.0657

Asia WGS AF: 0.174 AC: 599 AN: 3454

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.33
DANN	Benign	0.59
PhyloP100		-0.78
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: rs1527483; hg19: chr7-80301500;