chr10-43573110-A-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001099282.2(ZNF239):c.-216+527T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,018 control chromosomes in the GnomAD database, including 16,424 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 0.45 ( 16424 hom., cov: 32)
Consequence
ZNF239
NM_001099282.2 intron
NM_001099282.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.179
Publications
9 publications found
Genes affected
ZNF239 (HGNC:13031): (zinc finger protein 239) MOK2 proteins are DNA- and RNA-binding proteins that are mainly associated with nuclear RNP components, including the nucleoli and extranucleolar structures (Arranz et al., 1997 [PubMed 9121460]).[supplied by OMIM, Mar 2008]
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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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF239 | ENST00000374446.7 | c.-216+527T>G | intron_variant | Intron 2 of 3 | 1 | NM_001099282.2 | ENSP00000363569.1 | |||
ZNF239 | ENST00000426961.1 | c.-216+1430T>G | intron_variant | Intron 1 of 2 | 2 | ENSP00000398202.1 | ||||
ZNF239 | ENST00000535642.5 | c.-93+1430T>G | intron_variant | Intron 1 of 1 | 2 | ENSP00000443907.1 | ||||
ZNF239 | ENST00000491188.1 | n.58+1430T>G | intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.445 AC: 67662AN: 151900Hom.: 16420 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
67662
AN:
151900
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: 0.445 AC: 67689AN: 152018Hom.: 16424 Cov.: 32 AF XY: 0.452 AC XY: 33577AN XY: 74290 show subpopulations
GnomAD4 genome
AF:
AC:
67689
AN:
152018
Hom.:
Cov.:
32
AF XY:
AC XY:
33577
AN XY:
74290
show subpopulations
African (AFR)
AF:
AC:
10184
AN:
41480
American (AMR)
AF:
AC:
7146
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
AC:
1616
AN:
3466
East Asian (EAS)
AF:
AC:
2777
AN:
5152
South Asian (SAS)
AF:
AC:
2632
AN:
4822
European-Finnish (FIN)
AF:
AC:
6459
AN:
10562
Middle Eastern (MID)
AF:
AC:
156
AN:
294
European-Non Finnish (NFE)
AF:
AC:
35201
AN:
67950
Other (OTH)
AF:
AC:
1000
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1818
3636
5453
7271
9089
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
630
1260
1890
2520
3150
<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:
1902
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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