7-80546290-A-G

Position:

• chr7-80546290-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007060402.1(LOC124901685):​n.146+23A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,988 control chromosomes in the GnomAD database, including 21,660 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.53 (21655 hom., cov: 32)
  • Exomes 𝑓: 0.53 (5 hom.)
• Consequence: LOC124901685 XR_007060402.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

LOC124901685 (HGNC:):

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901685	XR_007060402.1	n.146+23A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000435819.5	c.-184+23A>G		intron_variant		2		ENSP00000399421	P1
CD36	ENST00000648416.1	n.132+23A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80198 AN: 151840 Hom.: 21635 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.533

GnomAD4 exome AF: 0.533 AC: 16 AN: 30 Hom.: 5 Cov.: 0 AF XY: 0.538 AC XY: 14 AN XY: 26

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.577

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.528 AC: 80271 AN: 151958 Hom.: 21655 Cov.: 32 AF XY: 0.528 AC XY: 39189 AN XY: 74254

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.536

Alfa AF: 0.497 Hom.: 2372

Bravo AF: 0.531

Asia WGS AF: 0.695 AC: 2413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs1194197; hg19: chr7-80175606;