chr7-80664600-C-T

Variant names:

• chr7-80664600-C-T
• rs3211908
• NM_001001548.3:c.701+103C>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.701+103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0632 in 759,756 control chromosomes in the GnomAD database, including 2,017 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.053 (327 hom., cov: 32)
  • Exomes 𝑓: 0.066 (1690 hom.)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.361
• Publications: 22 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=-0.81).
• BP6: Variant 7-80664600-C-T is Benign according to our data. Variant chr7-80664600-C-T is described in ClinVar as Benign. ClinVar VariationId is 1259835.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.701+103C>T		intron_variant	Intron 7 of 14	ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.701+103C>T		intron_variant	Intron 7 of 14	5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 8028 AN: 152004 Hom.: 327 Cov.: 32

Gnomad AFR AF: 0.0251

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.0934

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0513

Gnomad OTH AF: 0.0549

GnomAD4 exome AF: 0.0657 AC: 39947 AN: 607634 Hom.: 1690 AF XY: 0.0670 AC XY: 22096 AN XY: 329766

African (AFR) AF: 0.0254 AC: 433 AN: 17080

American (AMR) AF: 0.0852 AC: 3446 AN: 40436

Ashkenazi Jewish (ASJ) AF: 0.0633 AC: 1249 AN: 19736

East Asian (EAS) AF: 0.170 AC: 5885 AN: 34602

South Asian (SAS) AF: 0.0892 AC: 6044 AN: 67788

European-Finnish (FIN) AF: 0.0608 AC: 2935 AN: 48272

Middle Eastern (MID) AF: 0.0199 AC: 78 AN: 3920

European-Non Finnish (NFE) AF: 0.0519 AC: 17878 AN: 344334

Other (OTH) AF: 0.0635 AC: 1999 AN: 31466

GnomAD4 genome AF: 0.0528 AC: 8032 AN: 152122 Hom.: 327 Cov.: 32 AF XY: 0.0539 AC XY: 4007 AN XY: 74360

African (AFR) AF: 0.0250 AC: 1039 AN: 41528

American (AMR) AF: 0.0773 AC: 1182 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0580 AC: 201 AN: 3468

East Asian (EAS) AF: 0.189 AC: 976 AN: 5154

South Asian (SAS) AF: 0.0941 AC: 453 AN: 4812

European-Finnish (FIN) AF: 0.0532 AC: 564 AN: 10604

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0513 AC: 3490 AN: 67970

Other (OTH) AF: 0.0543 AC: 114 AN: 2098

Alfa AF: 0.0538 Hom.: 698

Bravo AF: 0.0504

Asia WGS AF: 0.146 AC: 505 AN: 3476

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

- -

Nov 10, 2018

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	-0.81
CADD	Benign	0.54
DANN	Benign	0.57
PhyloP100		-0.36
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: rs3211908; hg19: chr7-80293916; COSMIC: COSV59215759; COSMIC: COSV59215759;