rs5790842
Your query was ambiguous. Multiple possible variants found:
- chr11-30878716-TAAAAAA-T
- chr11-30878716-TAAAAAA-TA
- chr11-30878716-TAAAAAA-TAA
- chr11-30878716-TAAAAAA-TAAA
- chr11-30878716-TAAAAAA-TAAAA
- chr11-30878716-TAAAAAA-TAAAAA
- chr11-30878716-TAAAAAA-TAAAAAAA
- chr11-30878716-TAAAAAA-TAAAAAAAA
- chr11-30878716-TAAAAAA-TAAAAAAAAA
- chr11-30878716-TAAAAAA-TAAAAAAAAAA
- chr11-30878716-TAAAAAA-TAAAAAAAAAAA
- chr11-30878716-TAAAAAA-TAAAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001387274.1(DCDC1):c.5234-11_5234-6delTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000008 in 1,250,574 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: 8.0e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DCDC1
NM_001387274.1 splice_region, intron
NM_001387274.1 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.25
Publications
0 publications found
Genes affected
DCDC1 (HGNC:20625): (doublecortin domain containing 1) This gene encodes a member of the doublecortin family. The protein encoded by this gene is a hydrophilic, intracellular protein. It contains a single doublecortin domain and is unable to bind microtubules and to regulate microtubule polymerization. This gene is mainly expressed in adult testis. It does not have a mouse homolog. [provided by RefSeq, Sep 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001387274.1. 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 |
|---|---|---|---|---|---|---|---|---|---|
| DCDC1 | MANE Select | c.5234-11_5234-6delTTTTTT | splice_region intron | N/A | NP_001374203.1 | A0A804HJA9 | |||
| DCDC1 | c.5225-11_5225-6delTTTTTT | splice_region intron | N/A | NP_001354908.1 | M0R2J8-1 | ||||
| DCDC1 | c.2546-11_2546-6delTTTTTT | splice_region intron | N/A | NP_065920.2 | B6ZDN3 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DCDC1 | MANE Select | c.5234-11_5234-6delTTTTTT | splice_region intron | N/A | ENSP00000507427.1 | A0A804HJA9 | |||
| DCDC1 | TSL:5 | c.5225-11_5225-6delTTTTTT | splice_region intron | N/A | ENSP00000472625.1 | M0R2J8-1 | |||
| DCDC1 | TSL:5 | c.2546-11_2546-6delTTTTTT | splice_region intron | N/A | ENSP00000385936.3 | B6ZDN3 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 140190Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
0
AN:
140190
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: 8.00e-7 AC: 1AN: 1250574Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 619936 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
1250574
Hom.:
AF XY:
AC XY:
0
AN XY:
619936
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:
26356
American (AMR)
AF:
AC:
0
AN:
23918
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19474
East Asian (EAS)
AF:
AC:
0
AN:
33828
South Asian (SAS)
AF:
AC:
0
AN:
65640
European-Finnish (FIN)
AF:
AC:
0
AN:
41176
Middle Eastern (MID)
AF:
AC:
0
AN:
4394
European-Non Finnish (NFE)
AF:
AC:
1
AN:
984422
Other (OTH)
AF:
AC:
0
AN:
51366
⚠️ 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: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00 AC: 0AN: 140190Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 67790
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
140190
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
67790
African (AFR)
AF:
AC:
0
AN:
37310
American (AMR)
AF:
AC:
0
AN:
13966
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3380
East Asian (EAS)
AF:
AC:
0
AN:
4768
South Asian (SAS)
AF:
AC:
0
AN:
4378
European-Finnish (FIN)
AF:
AC:
0
AN:
8246
Middle Eastern (MID)
AF:
AC:
0
AN:
296
European-Non Finnish (NFE)
AF:
AC:
0
AN:
65072
Other (OTH)
AF:
AC:
0
AN:
1898
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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