11-44605107-G-A

Variant names:

• chr11-44605107-G-A
• rs34170190
• NM_002231.4:c.186G>A

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BS1 BS2

The NM_002231.4(CD82):​c.186G>A​(p.Val62Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00206 in 1,614,182 control chromosomes in the GnomAD database, including 75 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.011 (44 hom., cov: 33)
  • Exomes 𝑓: 0.0012 (31 hom.)
• Consequence: CD82 NM_002231.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.607
• Publications: 2 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]

CD82-AS1 (HGNC:56287): (CD82 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BP6: Variant 11-44605107-G-A is Benign according to our data. Variant chr11-44605107-G-A is described in ClinVar as Benign. ClinVar VariationId is 711550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.607 with no splicing effect.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0107 (1636/152298) while in subpopulation AFR AF = 0.0373 (1552/41564). AF 95% confidence interval is 0.0358. There are 44 homozygotes in GnomAd4. There are 770 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 44 AR gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD82	NM_002231.4	MANE Select	c.186G>A	p.Val62Val	synonymous	Exon 5 of 10	NP_002222.1	P27701-1
	CD82	NM_001024844.2		c.186G>A	p.Val62Val	synonymous	Exon 5 of 9	NP_001020015.1	P27701-2
	CD82-AS1	NR_182290.1		n.231C>T		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD82	ENST00000227155.9	TSL:1 MANE Select	c.186G>A	p.Val62Val	synonymous	Exon 5 of 10	ENSP00000227155.4	P27701-1
	CD82	ENST00000878578.1		c.186G>A	p.Val62Val	synonymous	Exon 5 of 10	ENSP00000548637.1
	CD82	ENST00000878563.1		c.186G>A	p.Val62Val	synonymous	Exon 5 of 10	ENSP00000548622.1

Frequencies

GnomAD3 genomes AF: 0.0107 AC: 1634 AN: 152180 Hom.: 44 Cov.: 33

Gnomad AFR AF: 0.0374

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00366

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00526

GnomAD2 exomes AF: 0.00297 AC: 739 AN: 249164 AF XY: 0.00213

Gnomad AFR exome AF: 0.0384

Gnomad AMR exome AF: 0.00223

Gnomad ASJ exome AF: 0.00119

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000135

Gnomad OTH exome AF: 0.00147

GnomAD4 exome AF: 0.00116 AC: 1691 AN: 1461884 Hom.: 31 Cov.: 32 AF XY: 0.000993 AC XY: 722 AN XY: 727242

African (AFR) AF: 0.0393 AC: 1315 AN: 33480

American (AMR) AF: 0.00228 AC: 102 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.000727 AC: 19 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.000104 AC: 9 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53414

Middle Eastern (MID) AF: 0.00277 AC: 16 AN: 5768

European-Non Finnish (NFE) AF: 0.0000674 AC: 75 AN: 1112008

Other (OTH) AF: 0.00257 AC: 155 AN: 60396

GnomAD4 genome AF: 0.0107 AC: 1636 AN: 152298 Hom.: 44 Cov.: 33 AF XY: 0.0103 AC XY: 770 AN XY: 74464

African (AFR) AF: 0.0373 AC: 1552 AN: 41564

American (AMR) AF: 0.00372 AC: 57 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3466

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5166

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000162 AC: 11 AN: 68024

Other (OTH) AF: 0.00520 AC: 11 AN: 2114

Alfa AF: 0.00574 Hom.: 6

Bravo AF: 0.0125

EpiCase AF: 0.000109

EpiControl AF: 0.000178

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.91
PhyloP100		0.61
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=99/1	polymorphism

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: rs34170190; hg19: chr11-44626657; COSMIC: COSV57036349; COSMIC: COSV57036349;