rs1344709

Positions:

• chr11-44572256-C-T

Variant summary

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

The ENST00000227155.9(CD82):​c.-103+6520C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,046 control chromosomes in the GnomAD database, including 24,834 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 0.56 (24834 hom., cov: 33)
• Consequence: CD82 ENST00000227155.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

CD82 (HGNC:6210): (CD82 molecule) This metastasis suppressor gene product is a membrane glycoprotein that is a member of the transmembrane 4 superfamily. Expression of this gene has been shown to be downregulated in tumor progression of human cancers and can be activated by p53 through a consensus binding sequence in the promoter. Its expression and that of p53 are strongly correlated, and the loss of expression of these two proteins is associated with poor survival for prostate cancer patients. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD82	NM_002231.4	c.-103+6520C>T		intron_variant		ENST00000227155.9	NP_002222.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD82	ENST00000227155.9	c.-103+6520C>T		intron_variant		1	NM_002231.4	ENSP00000227155	P1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85455 AN: 151926 Hom.: 24799 Cov.: 33

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.565

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.563 AC: 85530 AN: 152046 Hom.: 24834 Cov.: 33 AF XY: 0.562 AC XY: 41765 AN XY: 74318

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.559

Alfa AF: 0.549 Hom.: 11297

Bravo AF: 0.561

Asia WGS AF: 0.297 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.42

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: rs1344709; hg19: chr11-44593806;