chr20-1978880-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_024411.5(PDYN):c.*1443G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0063 in 152,278 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0063 ( 9 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
PDYN
NM_024411.5 3_prime_UTR
NM_024411.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0700
Publications
0 publications found
Genes affected
PDYN (HGNC:8820): (prodynorphin) The protein encoded by this gene is a preproprotein that is proteolytically processed to form the secreted opioid peptides beta-neoendorphin, dynorphin, leu-enkephalin, rimorphin, and leumorphin. These peptides are ligands for the kappa-type of opioid receptor. Dynorphin is involved in modulating responses to several psychoactive substances, including cocaine. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2010]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -16 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 20-1978880-C-T is Benign according to our data. Variant chr20-1978880-C-T is described in ClinVar as Benign. ClinVar VariationId is 337807.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 960 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_024411.5. 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 |
|---|---|---|---|---|---|---|---|---|---|
| PDYN | NM_024411.5 | MANE Select | c.*1443G>A | 3_prime_UTR | Exon 4 of 4 | NP_077722.1 | P01213 | ||
| PDYN | NM_001190892.1 | c.*1443G>A | 3_prime_UTR | Exon 3 of 3 | NP_001177821.1 | P01213 | |||
| PDYN | NM_001190898.3 | c.*1443G>A | 3_prime_UTR | Exon 4 of 4 | NP_001177827.1 | P01213 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PDYN | ENST00000217305.3 | TSL:1 MANE Select | c.*1443G>A | 3_prime_UTR | Exon 4 of 4 | ENSP00000217305.2 | P01213 | ||
| PDYN | ENST00000539905.5 | TSL:4 | c.*1443G>A | 3_prime_UTR | Exon 3 of 3 | ENSP00000440185.1 | P01213 | ||
| PDYN | ENST00000540134.5 | TSL:4 | c.*1443G>A | 3_prime_UTR | Exon 4 of 4 | ENSP00000442259.1 | P01213 |
Frequencies
GnomAD3 genomes 0.00632 AC: 962AN: 152160Hom.: 10 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
962
AN:
152160
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: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome 0.00630 AC: 960AN: 152278Hom.: 9 Cov.: 32 AF XY: 0.00655 AC XY: 488AN XY: 74466 show subpopulations
GnomAD4 genome
AF:
AC:
960
AN:
152278
Hom.:
Cov.:
32
AF XY:
AC XY:
488
AN XY:
74466
show subpopulations
African (AFR)
AF:
AC:
64
AN:
41552
American (AMR)
AF:
AC:
60
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
77
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5186
South Asian (SAS)
AF:
AC:
7
AN:
4828
European-Finnish (FIN)
AF:
AC:
206
AN:
10604
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
512
AN:
68022
Other (OTH)
AF:
AC:
15
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
50
100
151
201
251
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
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20
40
60
80
100
<30
30-35
35-40
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Benign
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
-
-
1
Spinocerebellar ataxia type 23 (1)
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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