rs3211956

Variant names:

• chr7-80674446-T-G
• rs3211956
• NM_001001548.3:c.1419+299T>G

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.1419+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, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.11
• Publications: 23 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 -20 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 VariationId is 1240468.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001548.3	MANE Select	c.1419+299T>G		intron	N/A	NP_001001548.1	P16671-1
	CD36	NM_001371075.1		c.1419+299T>G		intron	N/A	NP_001358004.1	P16671-1
	CD36	NM_001371077.1		c.1419+299T>G		intron	N/A	NP_001358006.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.1419+299T>G		intron	N/A	ENSP00000415743.2	P16671-1
	CD36	ENST00000464213.1	TSL:1	n.3285+299T>G		intron	N/A
	CD36	ENST00000855930.1		c.*299T>G		3_prime_UTR	Exon 14 of 14	ENSP00000525989.1

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

African (AFR) AF: 0.0266 AC: 141 AN: 5298

American (AMR) AF: 0.0801 AC: 501 AN: 6252

Ashkenazi Jewish (ASJ) AF: 0.0829 AC: 423 AN: 5102

East Asian (EAS) AF: 0.245 AC: 2107 AN: 8606

South Asian (SAS) AF: 0.109 AC: 3081 AN: 28296

European-Finnish (FIN) AF: 0.0676 AC: 547 AN: 8086

Middle Eastern (MID) AF: 0.0360 AC: 26 AN: 722

European-Non Finnish (NFE) AF: 0.0791 AC: 8768 AN: 110854

Other (OTH) AF: 0.0882 AC: 855 AN: 9692

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

African (AFR) AF: 0.0279 AC: 1160 AN: 41544

American (AMR) AF: 0.0818 AC: 1247 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0792 AC: 275 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1292 AN: 5166

South Asian (SAS) AF: 0.113 AC: 544 AN: 4824

European-Finnish (FIN) AF: 0.0607 AC: 644 AN: 10610

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0791 AC: 5371 AN: 67876

Other (OTH) AF: 0.0753 AC: 159 AN: 2112

Alfa AF: 0.0766 Hom.: 531

Bravo AF: 0.0667

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.13
DANN	Benign	0.80
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3211956; hg19: chr7-80303762;