rs3211956

chr7-80674446-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001001548.3(CD36):c.*299T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 334,970 control chromosomes in the GnomAD database, including 1,462 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.070 (532 hom., cov: 32)
  • Exomes 𝑓: 0.090 (930 hom.)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.11

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 7-80674446-T-G is Benign according to our data. Variant chr7-80674446-T-G is described in ClinVar as [Benign]. Clinvar id is 1240468.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001548.3	c.*299T>G		intron_variant		ENST00000447544.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000447544.7	c.*299T>G		intron_variant		5	NM_001001548.3	P1

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10719 AN: 151944 Hom.: 533 Cov.: 32

Gnomad AFR AF: 0.0280

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.0792

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.0751

GnomAD4 exome AF: 0.0899 AC: 16449 AN: 182908 Hom.: 930 Cov.: 0 AF XY: 0.0930 AC XY: 9209 AN XY: 99064

Gnomad4 AFR exome AF: 0.0266

Gnomad4 AMR exome AF: 0.0801

Gnomad4 ASJ exome AF: 0.0829

Gnomad4 EAS exome AF: 0.245

Gnomad4 SAS exome AF: 0.109

Gnomad4 FIN exome AF: 0.0676

Gnomad4 NFE exome AF: 0.0791

Gnomad4 OTH exome AF: 0.0882

GnomAD4 genome AF: 0.0705 AC: 10718 AN: 152062 Hom.: 532 Cov.: 32 AF XY: 0.0711 AC XY: 5282 AN XY: 74338

Gnomad4 AFR AF: 0.0279

Gnomad4 AMR AF: 0.0818

Gnomad4 ASJ AF: 0.0792

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0607

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.0753

Alfa AF: 0.0776 Hom.: 482

Bravo AF: 0.0667

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.13
Dann	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3211956; hg19: chr7-80303762;