rs3211913

Variant names:

• chr7-80665288-A-G
• rs3211913
• NM_001001548.3:c.701+791A>G

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The NM_001001548.3(CD36):c.701+791A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.124 (AC=18,789) in the gnomAD database across 151,914 control chromosomes, including 2,803 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.35. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (2803 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 7 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

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Benign. The variant received -12 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); Splicing verdict: benign (Strong).; Germline computational verdict: benign (Strong).
	BA1Stand-alone benign allele frequency (>5%)		GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.3499 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_001001548.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	CD36 NM_001001548.3	MANE Select	c.701+791A>G	intron	Intron 7 of 14	Prot: NP_001001548.1 UniProt:
	CD36 NM_000072.3		c.701+791A>G	intron	Intron 7 of 13	Prot: NP_000063.2 UniProt:
	CD36 NM_001001547.3		c.701+791A>G	intron	Intron 7 of 13	Prot: NP_001001547.1 UniProt:

CD36 NM_001001548.3

MANE Select

HGVSc / HGVSpc.701+791A>G

Exon rankIntron 7 of 14

intron

Prot: NP_001001548.1UniProt: P16671-1A4D1B1

CD36 NM_000072.3

HGVSc / HGVSpc.701+791A>G

Exon rankIntron 7 of 13

intron

Prot: NP_000063.2UniProt: P16671-1A4D1B1

CD36 NM_001001547.3

HGVSc / HGVSpc.701+791A>G

Exon rankIntron 7 of 13

intron

Prot: NP_001001547.1UniProt: A4D1B1P16671-1

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	CD36 ENST00000447544.7	TSL:5MANE Select	c.701+791A>G	intron	Intron 7 of 14	Prot: ENSP00000415743.2 UniProt:
	CD36 ENST00000309881.11	TSL:1	c.701+791A>G	intron	Intron 7 of 13	Prot: ENSP00000308165.7 UniProt:
	CD36 ENST00000394788.7	TSL:1	c.701+791A>G	intron	Intron 7 of 13	Prot: ENSP00000378268.3 UniProt:

CD36 ENST00000447544.7

TSL:5MANE Select

HGVSc / HGVSpc.701+791A>G

Exon rankIntron 7 of 14

intron

Prot: ENSP00000415743.2UniProt: P16671-1

CD36 ENST00000309881.11

TSL:1

HGVSc / HGVSpc.701+791A>G

Exon rankIntron 7 of 13

intron

Prot: ENSP00000308165.7UniProt: P16671-1

CD36 ENST00000394788.7

TSL:1

HGVSc / HGVSpc.701+791A>G

Exon rankIntron 7 of 13

intron

Prot: ENSP00000378268.3UniProt: P16671-1

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.123	AC:18724	Hom:2783	AN:151798	Cov:32
GnomAD4 genome	AF: 0.124	AC:18789	Hom:2803	AN:151914	Cov:32
TOPMed (Bravo)	AF: 0.141	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.0926	AC:3583	Hom:450	AN:38714	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.118	AC:276	Hom:30	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.0744	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.0300	AC:9	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.0740	AC:256	Hom:	AN:3450	Cov:
Korea4K (4,157 Koreans)	AF: 0.0860	AC:620	Hom:	AN:7218	Cov:
Qatari Genome	AF: 0.102	AC:18	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.130	AC:15837	Hom:1029	AN:121740	Cov:
Turkish Variome	AF: 0.0233	AC:36	Hom:1	AN:1546	Cov:
UK10K	AF: 0.0206	AC:156	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.0807	AC:723	Hom:39	AN:8960	Cov:

Showing 14 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	1.7
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.77
GPN-Star LLR	N/A	3.8
GPN-Star score	N/A	-0.51
Mutation Taster	N/A	100/0	polymorphism (auto)
PhyloP100	Benign	-0.94

Showing 8 of 8 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs3211913;

hg19: chr7-80294604;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar