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GeneBe

11-44618696-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_002231.4(CD82):c.699C>T(p.Gly233=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0022 in 1,613,228 control chromosomes in the GnomAD database, including 73 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.011 ( 34 hom., cov: 31)
Exomes 𝑓: 0.0012 ( 39 hom. )

Consequence

CD82
NM_002231.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.35
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-44618696-C-T is Benign according to our data. Variant chr11-44618696-C-T is described in ClinVar as [Benign]. Clinvar id is 786594.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.35 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0115 (1742/152092) while in subpopulation AFR AF= 0.038 (1579/41514). AF 95% confidence interval is 0.0365. There are 34 homozygotes in gnomad4. There are 818 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 34 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CD82NM_002231.4 linkuse as main transcriptc.699C>T p.Gly233= synonymous_variant 9/10 ENST00000227155.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CD82ENST00000227155.9 linkuse as main transcriptc.699C>T p.Gly233= synonymous_variant 9/101 NM_002231.4 P1P27701-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0114
AC:
1736
AN:
151976
Hom.:
34
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0380
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00864
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000390
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.00864
GnomAD3 exomes
AF:
0.00290
AC:
728
AN:
250618
Hom.:
8
AF XY:
0.00224
AC XY:
303
AN XY:
135548
show subpopulations
Gnomad AFR exome
AF:
0.0382
Gnomad AMR exome
AF:
0.00220
Gnomad ASJ exome
AF:
0.0000994
Gnomad EAS exome
AF:
0.000544
Gnomad SAS exome
AF:
0.000163
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000971
Gnomad OTH exome
AF:
0.000818
GnomAD4 exome
AF:
0.00123
AC:
1803
AN:
1461136
Hom.:
39
Cov.:
33
AF XY:
0.00109
AC XY:
789
AN XY:
726890
show subpopulations
Gnomad4 AFR exome
AF:
0.0418
Gnomad4 AMR exome
AF:
0.00212
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.000328
Gnomad4 SAS exome
AF:
0.000197
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000971
Gnomad4 OTH exome
AF:
0.00263
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0115
AC:
1742
AN:
152092
Hom.:
34
Cov.:
31
AF XY:
0.0110
AC XY:
818
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.0380
Gnomad4 AMR
AF:
0.00863
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000391
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.00855
Alfa
AF:
0.00469
Hom.:
4
Bravo
AF:
0.0130
Asia WGS
AF:
0.00173
AC:
6
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeOct 19, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
9.7
Dann
Benign
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs79095986; hg19: chr11-44640246; COSMIC: COSV99907463; COSMIC: COSV99907463; API