NM_001195215.2:c.82+19758G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001195215.2(DENND1B):c.82+19758G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,720 control chromosomes in the GnomAD database, including 4,242 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 0.23 ( 4242 hom., cov: 32)
Consequence
DENND1B
NM_001195215.2 intron
NM_001195215.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.34
Publications
17 publications found
Genes affected
DENND1B (HGNC:28404): (DENN domain containing 1B) Clathrin (see MIM 118955)-mediated endocytosis is a major mechanism for internalization of proteins and lipids. Members of the connecdenn family, such as DENND1B, function as guanine nucleotide exchange factors (GEFs) for the early endosomal small GTPase RAB35 (MIM 604199) and bind to clathrin and clathrin adaptor protein-2 (AP2; see MIM 601024). Thus, connecdenns link RAB35 activation with the clathrin machinery (Marat and McPherson, 2010 [PubMed 20154091]).[supplied by OMIM, Nov 2010]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.226 AC: 34242AN: 151602Hom.: 4238 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
34242
AN:
151602
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.226 AC: 34262AN: 151720Hom.: 4242 Cov.: 32 AF XY: 0.221 AC XY: 16368AN XY: 74174 show subpopulations
GnomAD4 genome
AF:
AC:
34262
AN:
151720
Hom.:
Cov.:
32
AF XY:
AC XY:
16368
AN XY:
74174
show subpopulations
African (AFR)
AF:
AC:
11439
AN:
41178
American (AMR)
AF:
AC:
3086
AN:
15252
Ashkenazi Jewish (ASJ)
AF:
AC:
659
AN:
3470
East Asian (EAS)
AF:
AC:
1068
AN:
5172
South Asian (SAS)
AF:
AC:
1182
AN:
4822
European-Finnish (FIN)
AF:
AC:
1436
AN:
10552
Middle Eastern (MID)
AF:
AC:
97
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14691
AN:
67968
Other (OTH)
AF:
AC:
493
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1346
2692
4039
5385
6731
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
368
736
1104
1472
1840
<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.:
Bravo
AF:
Asia WGS
AF:
AC:
954
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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