NM_001001548.3:c.1126-150C>A

Variant names:

• chr7-80672620-C-A
• rs1405747
• NM_001001548.3:c.1126-150C>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.1126-150C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 622,158 control chromosomes in the GnomAD database, including 58,529 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.40 (12254 hom., cov: 33)
  • Exomes 𝑓: 0.44 (46275 hom.)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.388
• Publications: 6 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=-0.93).
• BP6: Variant 7-80672620-C-A is Benign according to our data. Variant chr7-80672620-C-A is described in ClinVar as Benign. ClinVar VariationId is 1294701.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001548.3	MANE Select	c.1126-150C>A		intron	N/A	NP_001001548.1
	CD36	NM_000072.3		c.1126-150C>A		intron	N/A	NP_000063.2
	CD36	NM_001001547.3		c.1126-150C>A		intron	N/A	NP_001001547.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.1126-150C>A		intron	N/A	ENSP00000415743.2
	CD36	ENST00000309881.11	TSL:1	c.1126-150C>A		intron	N/A	ENSP00000308165.7
	CD36	ENST00000394788.7	TSL:1	c.1126-150C>A		intron	N/A	ENSP00000378268.3

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60165 AN: 151336 Hom.: 12240 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.445

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.401

GnomAD4 exome AF: 0.439 AC: 206765 AN: 470700 Hom.: 46275 AF XY: 0.441 AC XY: 111179 AN XY: 251974

African (AFR) AF: 0.304 AC: 3871 AN: 12742

American (AMR) AF: 0.336 AC: 7746 AN: 23074

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 5996 AN: 14386

East Asian (EAS) AF: 0.557 AC: 16822 AN: 30220

South Asian (SAS) AF: 0.449 AC: 20811 AN: 46332

European-Finnish (FIN) AF: 0.445 AC: 17652 AN: 39670

Middle Eastern (MID) AF: 0.438 AC: 834 AN: 1902

European-Non Finnish (NFE) AF: 0.440 AC: 121555 AN: 276268

Other (OTH) AF: 0.440 AC: 11478 AN: 26106

GnomAD4 genome AF: 0.397 AC: 60204 AN: 151458 Hom.: 12254 Cov.: 33 AF XY: 0.398 AC XY: 29414 AN XY: 73974

African (AFR) AF: 0.301 AC: 12474 AN: 41400

American (AMR) AF: 0.355 AC: 5396 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1412 AN: 3414

East Asian (EAS) AF: 0.530 AC: 2738 AN: 5162

South Asian (SAS) AF: 0.456 AC: 2203 AN: 4826

European-Finnish (FIN) AF: 0.448 AC: 4706 AN: 10508

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.442 AC: 29903 AN: 67628

Other (OTH) AF: 0.406 AC: 851 AN: 2098

Alfa AF: 0.426 Hom.: 2794

Bravo AF: 0.385

Asia WGS AF: 0.504 AC: 1743 AN: 3464

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.66
DANN	Benign	0.53
PhyloP100		-0.39
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: rs1405747; hg19: chr7-80301936;