rs1344709

Variant names:

• chr11-44572256-C-T
• rs1344709
• NM_002231.4:c.-103+6520C>T

Variant summary

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

The NM_002231.4(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 NM_002231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 6 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=-0.93).
• 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 rank	MANE	Protein	UniProt
CD82	NM_002231.4	c.-103+6520C>T		intron_variant	Intron 1 of 9	ENST00000227155.9	NP_002222.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD82	ENST00000227155.9	c.-103+6520C>T		intron_variant	Intron 1 of 9	1	NM_002231.4	ENSP00000227155.4

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

African (AFR) AF: 0.645 AC: 26746 AN: 41466

American (AMR) AF: 0.519 AC: 7935 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2224 AN: 3468

East Asian (EAS) AF: 0.191 AC: 989 AN: 5172

South Asian (SAS) AF: 0.435 AC: 2100 AN: 4826

European-Finnish (FIN) AF: 0.573 AC: 6063 AN: 10576

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37812 AN: 67928

Other (OTH) AF: 0.559 AC: 1181 AN: 2112

Alfa AF: 0.551 Hom.: 12673

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
PhyloP100		0.15
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: rs1344709; hg19: chr11-44593806;