rs11243354
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000496611.2(DPP6):c.*350T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,007,696 control chromosomes in the GnomAD database, including 23,340 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.27 ( 6990 hom., cov: 32)
Exomes 𝑓: 0.18 ( 16350 hom. )
Consequence
DPP6
ENST00000496611.2 3_prime_UTR
ENST00000496611.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0380
Publications
2 publications found
Genes affected
DPP6 (HGNC:3010): (dipeptidyl peptidase like 6) This gene encodes a single-pass type II membrane protein that is a member of the peptidase S9B family of serine proteases. This protein has no detectable protease activity, most likely due to the absence of the conserved serine residue normally present in the catalytic domain of serine proteases. However, it does bind specific voltage-gated potassium channels and alters their expression and biophysical properties. Variations in this gene may be associated with susceptibility to amyotrophic lateral sclerosis and with idiopathic ventricular fibrillation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
DPP6 Gene-Disease associations (from GenCC):
- autosomal dominant primary microcephalyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- paroxysmal familial ventricular fibrillationInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- intellectual disability, autosomal dominant 33Inheritance: AD, Unknown Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- ventricular fibrillation, paroxysmal familial, 2Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- complex neurodevelopmental disorderInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 7-154587524-T-C is Benign according to our data. Variant chr7-154587524-T-C is described in ClinVar as [Benign]. Clinvar id is 1237202.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.266 AC: 40351AN: 151670Hom.: 6969 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
40351
AN:
151670
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 AF: 0.184 AC: 157485AN: 855908Hom.: 16350 Cov.: 11 AF XY: 0.183 AC XY: 78904AN XY: 431360 show subpopulations
GnomAD4 exome
AF:
AC:
157485
AN:
855908
Hom.:
Cov.:
11
AF XY:
AC XY:
78904
AN XY:
431360
show subpopulations
African (AFR)
AF:
AC:
10742
AN:
20876
American (AMR)
AF:
AC:
5841
AN:
24328
Ashkenazi Jewish (ASJ)
AF:
AC:
2470
AN:
16982
East Asian (EAS)
AF:
AC:
2277
AN:
33056
South Asian (SAS)
AF:
AC:
9187
AN:
55302
European-Finnish (FIN)
AF:
AC:
4736
AN:
30278
Middle Eastern (MID)
AF:
AC:
725
AN:
4400
European-Non Finnish (NFE)
AF:
AC:
113493
AN:
630992
Other (OTH)
AF:
AC:
8014
AN:
39694
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
6787
13574
20361
27148
33935
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.266 AC: 40423AN: 151788Hom.: 6990 Cov.: 32 AF XY: 0.262 AC XY: 19434AN XY: 74196 show subpopulations
GnomAD4 genome
AF:
AC:
40423
AN:
151788
Hom.:
Cov.:
32
AF XY:
AC XY:
19434
AN XY:
74196
show subpopulations
African (AFR)
AF:
AC:
20490
AN:
41298
American (AMR)
AF:
AC:
4024
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
AC:
475
AN:
3466
East Asian (EAS)
AF:
AC:
436
AN:
5124
South Asian (SAS)
AF:
AC:
740
AN:
4804
European-Finnish (FIN)
AF:
AC:
1547
AN:
10548
Middle Eastern (MID)
AF:
AC:
57
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11974
AN:
67980
Other (OTH)
AF:
AC:
487
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
1351
2703
4054
5406
6757
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
510
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
May 11, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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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