rs11301800
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr5-119165286-TAAAAAAAAAAA-T
- chr5-119165286-TAAAAAAAAAAA-TAA
- chr5-119165286-TAAAAAAAAAAA-TAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAAAAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAAAAAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAAAAAAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAAAAAAAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAAAAAAAAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAAAAAAAAAAAAA
- chr5-119165286-TAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The ENST00000539542.6(DMXL1):c.4970+7_4970+17delAAAAAAAAAAA variant causes a splice region, intron change. The variant allele was found at a frequency of 0.0000124 in 884,614 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000010 ( 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: 4.04
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+14_4970+24delAAAAAAAAAAA | intron | N/A | NP_001277250.1 | F5H269 | ||
| DMXL1 | NM_001349239.2 | c.4970+14_4970+24delAAAAAAAAAAA | intron | N/A | NP_001336168.1 | F5H269 | |||
| DMXL1 | NM_001349240.2 | c.4970+14_4970+24delAAAAAAAAAAA | 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+7_4970+17delAAAAAAAAAAA | splice_region intron | N/A | ENSP00000439479.1 | F5H269 | ||
| DMXL1 | ENST00000311085.8 | TSL:1 | c.4970+7_4970+17delAAAAAAAAAAA | splice_region intron | N/A | ENSP00000309690.8 | Q9Y485 | ||
| DMXL1 | ENST00000939842.1 | c.4325+7_4325+17delAAAAAAAAAAA | splice_region intron | N/A | ENSP00000609901.1 |
Frequencies
GnomAD3 genomes 0.0000262 AC: 3AN: 114286Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
114286
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: 0.0000104 AC: 8AN: 770328Hom.: 0 AF XY: 0.0000150 AC XY: 6AN XY: 398892 show subpopulations
GnomAD4 exome
AF:
AC:
8
AN:
770328
Hom.:
AF XY:
AC XY:
6
AN XY:
398892
show subpopulations
African (AFR)
AF:
AC:
0
AN:
17838
American (AMR)
AF:
AC:
0
AN:
22268
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
16622
East Asian (EAS)
AF:
AC:
0
AN:
32276
South Asian (SAS)
AF:
AC:
0
AN:
47912
European-Finnish (FIN)
AF:
AC:
0
AN:
38062
Middle Eastern (MID)
AF:
AC:
0
AN:
2646
European-Non Finnish (NFE)
AF:
AC:
8
AN:
557914
Other (OTH)
AF:
AC:
0
AN:
34790
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.669
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
GnomAD4 genome 0.0000262 AC: 3AN: 114286Hom.: 0 Cov.: 0 AF XY: 0.0000366 AC XY: 2AN XY: 54660 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
114286
Hom.:
Cov.:
0
AF XY:
AC XY:
2
AN XY:
54660
show subpopulations
African (AFR)
AF:
AC:
0
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:
3
AN:
53342
Other (OTH)
AF:
AC:
0
AN:
1598
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.542
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<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:
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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