rs761084725
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr11-8776186-A-ACACACACACACACACACACC
- chr11-8776186-A-ACACACACACACACACC
- chr11-8776186-A-ACACACACACACACC
- chr11-8776186-A-ACACACACACACACACACACACACACACACC
- chr11-8776186-A-ACACACACACACACACACACACACACACC
- chr11-8776186-A-ACACACACACACACACACACACACACC
- chr11-8776186-A-ACACACACACACACACACACACACC
- chr11-8776186-A-ACACACACACACACACACACACC
- chr11-8776186-A-ACACACACACACACACACACCCC
- chr11-8776186-A-ACACACACACACACACACC
- chr11-8776186-A-ACACACACACACACACCCC
- chr11-8776186-A-ACACACACACACACCCC
- chr11-8776186-A-ACACACACACACC
- chr11-8776186-A-ACACACACACACCCC
- chr11-8776186-A-ACACACACACC
- chr11-8776186-A-ACACACACACCCC
- chr11-8776186-A-ACACACACC
- chr11-8776186-A-ACACACACCCC
- chr11-8776186-A-ACACACC
- chr11-8776186-A-ACACACCCC
- chr11-8776186-A-ACACACCCCCC
- chr11-8776186-A-ACACC
- chr11-8776186-A-ACACCCC
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_213618.2(DENND2B):c.-25-25462_-25-25461insGGTGTGTGTGTGTGTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00207 in 143,408 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0021 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00052 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
DENND2B
NM_213618.2 intron
NM_213618.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.461
Publications
0 publications found
Genes affected
DENND2B (HGNC:11350): (DENN domain containing 2B) This gene was identified by its ability to suppress the tumorigenicity of Hela cells in nude mice. The protein encoded by this gene contains a C-terminal region that shares similarity with the Rab 3 family of small GTP binding proteins. This protein preferentially binds to the SH3 domain of c-Abl kinase, and acts as a regulator of MAPK1/ERK2 kinase, which may contribute to its ability to reduce the tumorigenic phenotype in cells. Three alternatively spliced transcript variants of this gene encoding distinct isoforms are identified. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
BP6
Variant 11-8776186-A-ACACACACACACACACACACC is Benign according to our data. Variant chr11-8776186-A-ACACACACACACACACACACC is described in ClinVar as Benign. ClinVar VariationId is 2641585.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_213618.2. 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 |
|---|---|---|---|---|---|---|---|---|---|
| DENND2B | MANE Select | c.-25-25462_-25-25461insGGTGTGTGTGTGTGTGTGTG | intron | N/A | NP_998783.1 | P78524-1 | |||
| DENND2B | c.-25-25462_-25-25461insGGTGTGTGTGTGTGTGTGTG | intron | N/A | NP_001363424.1 | P78524-1 | ||||
| DENND2B | c.-25-25462_-25-25461insGGTGTGTGTGTGTGTGTGTG | intron | N/A | NP_001363425.1 | P78524-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DENND2B | TSL:1 MANE Select | c.-25-25462_-25-25461insGGTGTGTGTGTGTGTGTGTG | intron | N/A | ENSP00000319678.6 | P78524-1 | |||
| DENND2B | TSL:1 | c.-25-25462_-25-25461insGGTGTGTGTGTGTGTGTGTG | intron | N/A | ENSP00000433528.1 | P78524-1 | |||
| DENND2B | TSL:1 | c.-25-25462_-25-25461insGGTGTGTGTGTGTGTGTGTG | intron | N/A | ENSP00000435097.1 | P78524-2 |
Frequencies
GnomAD3 genomes 0.00207 AC: 297AN: 143290Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
297
AN:
143290
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000519 AC: 155AN: 298800Hom.: 1 Cov.: 0 AF XY: 0.000471 AC XY: 80AN XY: 169966 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
155
AN:
298800
Hom.:
Cov.:
0
AF XY:
AC XY:
80
AN XY:
169966
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
2
AN:
8512
American (AMR)
AF:
AC:
7
AN:
26882
Ashkenazi Jewish (ASJ)
AF:
AC:
5
AN:
10508
East Asian (EAS)
AF:
AC:
0
AN:
9214
South Asian (SAS)
AF:
AC:
22
AN:
58336
European-Finnish (FIN)
AF:
AC:
5
AN:
12290
Middle Eastern (MID)
AF:
AC:
1
AN:
2576
European-Non Finnish (NFE)
AF:
AC:
103
AN:
156450
Other (OTH)
AF:
AC:
10
AN:
14032
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.305
Heterozygous variant carriers
0
13
26
40
53
66
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00207 AC: 297AN: 143408Hom.: 0 Cov.: 32 AF XY: 0.00193 AC XY: 135AN XY: 70040 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
297
AN:
143408
Hom.:
Cov.:
32
AF XY:
AC XY:
135
AN XY:
70040
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
26
AN:
39180
American (AMR)
AF:
AC:
56
AN:
14592
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
3230
East Asian (EAS)
AF:
AC:
0
AN:
5012
South Asian (SAS)
AF:
AC:
5
AN:
4418
European-Finnish (FIN)
AF:
AC:
6
AN:
9894
Middle Eastern (MID)
AF:
AC:
1
AN:
266
European-Non Finnish (NFE)
AF:
AC:
190
AN:
63976
Other (OTH)
AF:
AC:
10
AN:
1962
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.395
Heterozygous variant carriers
0
14
27
41
54
68
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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