5-119165286-TAAAAAAAAAAA-TAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The ENST00000539542.6(DMXL1):c.4970+6_4970+7insAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000088 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
DMXL1
ENST00000539542.6 splice_region, intron
ENST00000539542.6 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.401
Publications
0 publications found
Genes affected
DMXL1 (HGNC:2937): (Dmx like 1) The protein encoded by this gene is a member of the WD repeat superfamily of proteins, which have regulatory functions. This gene is expressed in many tissue types including several types of eye tissue, and it has been associated with ocular phenotypes. In addition, it is upregulated in cultured cells that overexpress growth factor independence 1B, a transcription factor that is essential for hematopoietic cell development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000539542.6. 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 |
|---|---|---|---|---|---|---|---|---|---|
| DMXL1 | NM_001290321.3 | MANE Select | c.4970+22_4970+24dupAAA | intron | N/A | NP_001277250.1 | F5H269 | ||
| DMXL1 | NM_001349239.2 | c.4970+22_4970+24dupAAA | intron | N/A | NP_001336168.1 | F5H269 | |||
| DMXL1 | NM_001349240.2 | c.4970+22_4970+24dupAAA | intron | N/A | NP_001336169.1 | Q9Y485 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DMXL1 | ENST00000539542.6 | TSL:1 MANE Select | c.4970+6_4970+7insAAA | splice_region intron | N/A | ENSP00000439479.1 | F5H269 | ||
| DMXL1 | ENST00000311085.8 | TSL:1 | c.4970+6_4970+7insAAA | splice_region intron | N/A | ENSP00000309690.8 | Q9Y485 | ||
| DMXL1 | ENST00000939842.1 | c.4325+6_4325+7insAAA | splice_region intron | N/A | ENSP00000609901.1 |
Frequencies
GnomAD3 genomes 0.00000875 AC: 1AN: 114284Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
114284
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:
GnomAD4 exome AF: 0.000105 AC: 81AN: 770214Hom.: 0 Cov.: 0 AF XY: 0.000108 AC XY: 43AN XY: 398840 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
81
AN:
770214
Hom.:
Cov.:
0
AF XY:
AC XY:
43
AN XY:
398840
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
3
AN:
17836
American (AMR)
AF:
AC:
4
AN:
22266
Ashkenazi Jewish (ASJ)
AF:
AC:
3
AN:
16620
East Asian (EAS)
AF:
AC:
0
AN:
32274
South Asian (SAS)
AF:
AC:
17
AN:
47902
European-Finnish (FIN)
AF:
AC:
2
AN:
38060
Middle Eastern (MID)
AF:
AC:
2
AN:
2646
European-Non Finnish (NFE)
AF:
AC:
49
AN:
557824
Other (OTH)
AF:
AC:
1
AN:
34786
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.293
Heterozygous variant carriers
0
7
14
21
28
35
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
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00000875 AC: 1AN: 114284Hom.: 0 Cov.: 0 AF XY: 0.0000183 AC XY: 1AN XY: 54660 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
114284
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
54660
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
30460
American (AMR)
AF:
AC:
0
AN:
11428
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2814
East Asian (EAS)
AF:
AC:
0
AN:
4542
South Asian (SAS)
AF:
AC:
0
AN:
3622
European-Finnish (FIN)
AF:
AC:
0
AN:
5578
Middle Eastern (MID)
AF:
AC:
0
AN:
236
European-Non Finnish (NFE)
AF:
AC:
0
AN:
53342
Other (OTH)
AF:
AC:
0
AN:
1596
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
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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