rs10838316

chr11-44617105-G-Achr11-44617105-G-T

Variant summary

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

The NM_002231.4(CD82):c.439-1057G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,078 control chromosomes in the GnomAD database, including 3,654 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 0.19 (3654 hom., cov: 32)
• Consequence: CD82 NM_002231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD82	NM_002231.4	c.439-1057G>A		intron_variant		ENST00000227155.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD82	ENST00000227155.9	c.439-1057G>A		intron_variant		1	NM_002231.4	P1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29352 AN: 151958 Hom.: 3647 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.00636

Gnomad SAS AF: 0.0728

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.193 AC: 29385 AN: 152078 Hom.: 3654 Cov.: 32 AF XY: 0.187 AC XY: 13907 AN XY: 74338

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.00618

Gnomad4 SAS AF: 0.0726

Gnomad4 FIN AF: 0.0913

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.179

Alfa AF: 0.158 Hom.: 1049

Bravo AF: 0.203

Asia WGS AF: 0.0560 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.17
Dann	Benign	0.79

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: rs10838316; hg19: chr11-44638655;