NM_020162.4:c.1524+50G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020162.4(DHX33):c.1524+50G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 1,610,142 control chromosomes in the GnomAD database, including 27,268 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 0.15 ( 2838 hom., cov: 32)
Exomes 𝑓: 0.15 ( 24430 hom. )
Consequence
DHX33
NM_020162.4 intron
NM_020162.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.949
Publications
24 publications found
Genes affected
DHX33 (HGNC:16718): (DEAH-box helicase 33) This gene encodes a member of the DEAD box protein family. The DEAD box proteins are characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DHX33 | NM_020162.4 | c.1524+50G>A | intron_variant | Intron 9 of 11 | ENST00000225296.8 | NP_064547.2 | ||
DHX33 | NM_001199699.2 | c.1005+50G>A | intron_variant | Intron 8 of 10 | NP_001186628.1 | |||
DHX33 | XM_047436418.1 | c.1397-351G>A | intron_variant | Intron 8 of 8 | XP_047292374.1 | |||
DHX33 | XM_017024877.2 | c.240+50G>A | intron_variant | Intron 5 of 7 | XP_016880366.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.146 AC: 22179AN: 151924Hom.: 2844 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
22179
AN:
151924
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:
GnomAD2 exomes AF: 0.218 AC: 54491AN: 249538 AF XY: 0.214 show subpopulations
GnomAD2 exomes
AF:
AC:
54491
AN:
249538
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: 0.147 AC: 214439AN: 1458100Hom.: 24430 Cov.: 31 AF XY: 0.150 AC XY: 109108AN XY: 725344 show subpopulations
GnomAD4 exome
AF:
AC:
214439
AN:
1458100
Hom.:
Cov.:
31
AF XY:
AC XY:
109108
AN XY:
725344
show subpopulations
African (AFR)
AF:
AC:
1418
AN:
33374
American (AMR)
AF:
AC:
14987
AN:
44408
Ashkenazi Jewish (ASJ)
AF:
AC:
3693
AN:
25954
East Asian (EAS)
AF:
AC:
24965
AN:
39648
South Asian (SAS)
AF:
AC:
25230
AN:
85744
European-Finnish (FIN)
AF:
AC:
13379
AN:
53324
Middle Eastern (MID)
AF:
AC:
590
AN:
5726
European-Non Finnish (NFE)
AF:
AC:
120263
AN:
1109700
Other (OTH)
AF:
AC:
9914
AN:
60222
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.471
Heterozygous variant carriers
0
7230
14459
21689
28918
36148
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
4800
9600
14400
19200
24000
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.146 AC: 22186AN: 152042Hom.: 2838 Cov.: 32 AF XY: 0.159 AC XY: 11835AN XY: 74326 show subpopulations
GnomAD4 genome
AF:
AC:
22186
AN:
152042
Hom.:
Cov.:
32
AF XY:
AC XY:
11835
AN XY:
74326
show subpopulations
African (AFR)
AF:
AC:
2114
AN:
41474
American (AMR)
AF:
AC:
3634
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
AC:
471
AN:
3470
East Asian (EAS)
AF:
AC:
3309
AN:
5152
South Asian (SAS)
AF:
AC:
1507
AN:
4812
European-Finnish (FIN)
AF:
AC:
2897
AN:
10566
Middle Eastern (MID)
AF:
AC:
29
AN:
294
European-Non Finnish (NFE)
AF:
AC:
7844
AN:
67992
Other (OTH)
AF:
AC:
310
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
863
1726
2589
3452
4315
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
252
504
756
1008
1260
<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:
1526
AN:
3478
ClinVar
Not reported inComputational 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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