8-51372094-CA-CAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_144651.5(PXDNL):c.3693-16_3693-14dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000637 in 1,129,990 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000064 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PXDNL
NM_144651.5 intron
NM_144651.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.286
Publications
1 publications found
Genes affected
PXDNL (HGNC:26359): (peroxidasin like) Predicted to enable heme binding activity and peroxidase activity. Predicted to be involved in hydrogen peroxide catabolic process. Predicted to be located in cytoplasm. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PXDNL | ENST00000356297.5 | c.3693-16_3693-14dupTTT | intron_variant | Intron 18 of 22 | 1 | NM_144651.5 | ENSP00000348645.4 | |||
PXDNL | ENST00000522933.5 | c.912-16_912-14dupTTT | intron_variant | Intron 1 of 5 | 5 | ENSP00000428114.1 | ||||
PXDNL | ENST00000522628.5 | n.1491-16_1491-14dupTTT | intron_variant | Intron 2 of 4 | 2 | ENSP00000429855.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 148914Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
0
AN:
148914
Hom.:
Cov.:
0
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:
GnomAD2 exomes AF: 0.000219 AC: 23AN: 104804 AF XY: 0.000253 show subpopulations
GnomAD2 exomes
AF:
AC:
23
AN:
104804
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000637 AC: 72AN: 1129990Hom.: 0 Cov.: 28 AF XY: 0.0000447 AC XY: 25AN XY: 559846 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
72
AN:
1129990
Hom.:
Cov.:
28
AF XY:
AC XY:
25
AN XY:
559846
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
27378
American (AMR)
AF:
AC:
13
AN:
29300
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20918
East Asian (EAS)
AF:
AC:
0
AN:
30756
South Asian (SAS)
AF:
AC:
7
AN:
67240
European-Finnish (FIN)
AF:
AC:
0
AN:
41030
Middle Eastern (MID)
AF:
AC:
0
AN:
4606
European-Non Finnish (NFE)
AF:
AC:
50
AN:
860436
Other (OTH)
AF:
AC:
2
AN:
48326
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.239
Heterozygous variant carriers
0
13
26
38
51
64
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
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70-75
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>80
Age
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 148914Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 72548
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
148914
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
72548
African (AFR)
AF:
AC:
0
AN:
40004
American (AMR)
AF:
AC:
0
AN:
15028
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3438
East Asian (EAS)
AF:
AC:
0
AN:
5052
South Asian (SAS)
AF:
AC:
0
AN:
4742
European-Finnish (FIN)
AF:
AC:
0
AN:
9922
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67464
Other (OTH)
AF:
AC:
0
AN:
2040
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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