7-31775683-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001191057.4(PDE1C):c.1941G>A(p.Thr647Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,648 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
PDE1C
NM_001191057.4 synonymous
NM_001191057.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.30
Publications
0 publications found
Genes affected
PDE1C (HGNC:8776): (phosphodiesterase 1C) This gene encodes an enzyme that belongs to the 3'5'-cyclic nucleotide phosphodiesterase family. Members of this family catalyze hydrolysis of the cyclic nucleotides, cyclic adenosine monophosphate and cyclic guanosine monophosphate, to the corresponding nucleoside 5'-monophosphates. The enzyme encoded by this gene regulates proliferation and migration of vascular smooth muscle cells, and neointimal hyperplasia. This enzyme also plays a role in pathological vascular remodeling by regulating the stability of growth factor receptors, such as PDGF-receptor-beta. [provided by RefSeq, Jul 2016]
PDE1C Gene-Disease associations (from GenCC):
- autosomal dominant nonsyndromic hearing lossInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- hearing loss, autosomal dominant 74Inheritance: AD, Unknown Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
Variant 7-31775683-C-T is Benign according to our data. Variant chr7-31775683-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2657378.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.3 with no splicing effect.
BS2
High AC in GnomAdExome4 at 17 AD,Unknown gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001191057.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| PDE1C | NM_001191057.4 | MANE Select | c.1941G>A | p.Thr647Thr | synonymous | Exon 17 of 18 | NP_001177986.1 | Q14123-1 | |
| PDE1C | NM_001191058.4 | c.2121G>A | p.Thr707Thr | synonymous | Exon 18 of 19 | NP_001177987.2 | A0A0A0MS69 | ||
| PDE1C | NM_001191059.4 | c.1941G>A | p.Thr647Thr | synonymous | Exon 18 of 19 | NP_001177988.1 | Q14123-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PDE1C | ENST00000396191.6 | TSL:2 MANE Select | c.1941G>A | p.Thr647Thr | synonymous | Exon 17 of 18 | ENSP00000379494.1 | Q14123-1 | |
| PDE1C | ENST00000396193.5 | TSL:2 | c.2121G>A | p.Thr707Thr | synonymous | Exon 18 of 19 | ENSP00000379496.1 | A0A0A0MS69 | |
| PDE1C | ENST00000321453.12 | TSL:2 | c.1941G>A | p.Thr647Thr | synonymous | Exon 18 of 19 | ENSP00000318105.7 | Q14123-1 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152118
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: 0.0000116 AC: 17AN: 1460530Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 726544 show subpopulations
GnomAD4 exome
AF:
AC:
17
AN:
1460530
Hom.:
Cov.:
30
AF XY:
AC XY:
8
AN XY:
726544
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26134
East Asian (EAS)
AF:
AC:
0
AN:
39698
South Asian (SAS)
AF:
AC:
0
AN:
86252
European-Finnish (FIN)
AF:
AC:
0
AN:
52308
Middle Eastern (MID)
AF:
AC:
1
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
16
AN:
1111802
Other (OTH)
AF:
AC:
0
AN:
60364
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
2
3
5
6
8
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
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>80
Age
GnomAD4 genome 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74302 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152118
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74302
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41428
American (AMR)
AF:
AC:
0
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5178
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10598
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
68036
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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