11-44581778-A-G

Variant names:

• chr11-44581778-A-G
• rs730129
• NM_002231.4:c.-102-5697A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002231.4(CD82):​c.-102-5697A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,130 control chromosomes in the GnomAD database, including 34,279 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 0.67 (34279 hom., cov: 33)
• Consequence: CD82 NM_002231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850
• Publications: 7 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002231.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD82	NM_002231.4	MANE Select	c.-102-5697A>G		intron	N/A	NP_002222.1
	CD82	NM_001024844.2		c.-102-5697A>G		intron	N/A	NP_001020015.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD82	ENST00000227155.9	TSL:1 MANE Select	c.-102-5697A>G		intron	N/A	ENSP00000227155.4
	CD82	ENST00000342935.7	TSL:5	c.-102-5697A>G		intron	N/A	ENSP00000339686.3
	CD82	ENST00000527737.5	TSL:3	c.-60-3365A>G		intron	N/A	ENSP00000433151.1

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101783 AN: 152012 Hom.: 34275 Cov.: 33

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.669 AC: 101819 AN: 152130 Hom.: 34279 Cov.: 33 AF XY: 0.674 AC XY: 50095 AN XY: 74354

African (AFR) AF: 0.598 AC: 24801 AN: 41504

American (AMR) AF: 0.737 AC: 11269 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2768 AN: 3462

East Asian (EAS) AF: 0.836 AC: 4322 AN: 5168

South Asian (SAS) AF: 0.756 AC: 3645 AN: 4824

European-Finnish (FIN) AF: 0.660 AC: 6993 AN: 10596

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45821 AN: 67960

Other (OTH) AF: 0.687 AC: 1452 AN: 2114

Alfa AF: 0.678 Hom.: 160292

Bravo AF: 0.670

Asia WGS AF: 0.773 AC: 2690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.98
DANN	Benign	0.40
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs730129; hg19: chr11-44603328;