7-80615623-G-A

Variant names:

• chr7-80615623-G-A
• rs1761667
• ENST00000309881.11:c.-184+13244G>A

Variant summary

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

The NM_001001547.3(CD36):​c.-184+13244G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,986 control chromosomes in the GnomAD database, including 18,385 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (18385 hom., cov: 32)
• Consequence: CD36 NM_001001547.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.10
• Publications: 129 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: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 7-80615623-G-A is Benign according to our data. Variant chr7-80615623-G-A is described in ClinVar as Benign. ClinVar VariationId is 487078.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001547.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001547.3		c.-184+13244G>A		intron	N/A	NP_001001547.1	P16671-1
	CD36	NM_001371074.1		c.-180+13244G>A		intron	N/A	NP_001358003.1	P16671-1
	CD36	NM_001371075.1		c.-184+13244G>A		intron	N/A	NP_001358004.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000309881.11	TSL:1	c.-184+13244G>A		intron	N/A	ENSP00000308165.7	P16671-1
	CD36	ENST00000435819.5	TSL:2	c.-183-30465G>A		intron	N/A	ENSP00000399421.1	P16671-1
	CD36	ENST00000855923.1		c.-183-30465G>A		intron	N/A	ENSP00000525982.1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73410 AN: 151868 Hom.: 18377 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.483 AC: 73443 AN: 151986 Hom.: 18385 Cov.: 32 AF XY: 0.480 AC XY: 35654 AN XY: 74286

African (AFR) AF: 0.386 AC: 15995 AN: 41432

American (AMR) AF: 0.561 AC: 8563 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1894 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1610 AN: 5166

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4816

European-Finnish (FIN) AF: 0.526 AC: 5558 AN: 10558

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36770 AN: 67954

Other (OTH) AF: 0.500 AC: 1056 AN: 2110

Alfa AF: 0.519 Hom.: 2581

Bravo AF: 0.489

Asia WGS AF: 0.291 AC: 1016 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Type 2 diabetes mellitus (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.75
PhyloP100		-1.1
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: rs1761667; hg19: chr7-80244939;