chr11-103736010-G-A
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000533459.1(PDGFDDN):n.128-31112C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0523 in 152,260 control chromosomes in the GnomAD database, including 423 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 0.052 ( 423 hom., cov: 32)
Consequence
PDGFDDN
ENST00000533459.1 intron
ENST00000533459.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.301
Publications
1 publications found
Genes affected
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDGFDDN | ENST00000533459.1 | n.128-31112C>T | intron_variant | Intron 2 of 4 | 4 | |||||
PDGFDDN | ENST00000812819.1 | n.267-55668C>T | intron_variant | Intron 1 of 2 | ||||||
PDGFDDN | ENST00000812820.1 | n.149-55668C>T | intron_variant | Intron 1 of 3 | ||||||
PDGFDDN | ENST00000812821.1 | n.154-55668C>T | intron_variant | Intron 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.0523 AC: 7956AN: 152144Hom.: 419 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
7956
AN:
152144
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: 0.0523 AC: 7970AN: 152260Hom.: 423 Cov.: 32 AF XY: 0.0521 AC XY: 3881AN XY: 74438 show subpopulations
GnomAD4 genome
AF:
AC:
7970
AN:
152260
Hom.:
Cov.:
32
AF XY:
AC XY:
3881
AN XY:
74438
show subpopulations
African (AFR)
AF:
AC:
5092
AN:
41524
American (AMR)
AF:
AC:
480
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
45
AN:
3470
East Asian (EAS)
AF:
AC:
872
AN:
5166
South Asian (SAS)
AF:
AC:
250
AN:
4830
European-Finnish (FIN)
AF:
AC:
106
AN:
10622
Middle Eastern (MID)
AF:
AC:
16
AN:
292
European-Non Finnish (NFE)
AF:
AC:
1017
AN:
68032
Other (OTH)
AF:
AC:
90
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
376
753
1129
1506
1882
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
90
180
270
360
450
<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:
349
AN:
3478
ClinVar
Not reported inComputational 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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