rs1527463

Variant names:

• chr7-80647015-C-T
• rs1527463
• NM_001001548.3:c.120+155C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001001548.3(CD36):​c.120+155C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.977 in 728,100 control chromosomes in the GnomAD database, including 347,315 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.97 (71247 hom., cov: 32)
  • Exomes 𝑓: 0.98 (276068 hom.)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.314
• Publications: 3 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 7-80647015-C-T is Benign according to our data. Variant chr7-80647015-C-T is described in ClinVar as Benign. ClinVar VariationId is 1287973.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.120+155C>T		intron_variant	Intron 3 of 14	ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.120+155C>T		intron_variant	Intron 3 of 14	5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.967 AC: 147177 AN: 152184 Hom.: 71195 Cov.: 32

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.971

GnomAD4 exome AF: 0.979 AC: 563798 AN: 575798 Hom.: 276068 Cov.: 7 AF XY: 0.980 AC XY: 302038 AN XY: 308192

African (AFR) AF: 0.939 AC: 14153 AN: 15072

American (AMR) AF: 0.981 AC: 29361 AN: 29934

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 16391 AN: 17034

East Asian (EAS) AF: 1.00 AC: 30587 AN: 30588

South Asian (SAS) AF: 0.995 AC: 58853 AN: 59122

European-Finnish (FIN) AF: 0.980 AC: 33487 AN: 34182

Middle Eastern (MID) AF: 0.975 AC: 2105 AN: 2160

European-Non Finnish (NFE) AF: 0.978 AC: 349947 AN: 357968

Other (OTH) AF: 0.972 AC: 28914 AN: 29738

GnomAD4 genome AF: 0.967 AC: 147287 AN: 152302 Hom.: 71247 Cov.: 32 AF XY: 0.968 AC XY: 72071 AN XY: 74460

African (AFR) AF: 0.936 AC: 38890 AN: 41560

American (AMR) AF: 0.975 AC: 14896 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3347 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5183 AN: 5184

South Asian (SAS) AF: 0.996 AC: 4811 AN: 4832

European-Finnish (FIN) AF: 0.981 AC: 10419 AN: 10618

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.977 AC: 66492 AN: 68038

Other (OTH) AF: 0.971 AC: 2053 AN: 2114

Alfa AF: 0.972 Hom.: 21853

Bravo AF: 0.966

Asia WGS AF: 0.991 AC: 3446 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.40
PhyloP100		-0.31
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: rs1527463; hg19: chr7-80276331;