chr11-44617105-G-A

Variant names:

• chr11-44617105-G-A
• rs10838316
• NM_002231.4:c.439-1057G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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.439-1057G>A		intron	N/A	NP_002222.1
	CD82	NM_001024844.2		c.364-1057G>A		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.439-1057G>A		intron	N/A	ENSP00000227155.4
	CD82	ENST00000342935.7	TSL:5	c.364-1057G>A		intron	N/A	ENSP00000339686.3
	CD82	ENST00000530601.1	TSL:3	c.382-1057G>A		intron	N/A	ENSP00000433788.1

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

African (AFR) AF: 0.346 AC: 14360 AN: 41446

American (AMR) AF: 0.133 AC: 2030 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3468

East Asian (EAS) AF: 0.00618 AC: 32 AN: 5174

South Asian (SAS) AF: 0.0726 AC: 350 AN: 4820

European-Finnish (FIN) AF: 0.0913 AC: 966 AN: 10580

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10167 AN: 67976

Other (OTH) AF: 0.179 AC: 378 AN: 2114

Alfa AF: 0.183 Hom.: 2982

Bravo AF: 0.203

Asia WGS AF: 0.0560 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.17
DANN	Benign	0.79
PhyloP100		-1.1
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: rs10838316; hg19: chr11-44638655;