11-118755506-TAAAA-TAA
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_004397.6(DDX6):c.1175-5_1175-4delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000357 in 1,092,180 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as (no stars).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000036 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DDX6
NM_004397.6 splice_region, intron
NM_004397.6 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.19
Publications
0 publications found
Genes affected
DDX6 (HGNC:2747): (DEAD-box helicase 6) This gene encodes a member of the DEAD box protein family. The protein is an RNA helicase found in P-bodies and stress granules, and functions in translation suppression and mRNA degradation. It is required for microRNA-induced gene silencing. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Mar 2012]
DDX6 Gene-Disease associations (from GenCC):
- intellectual developmental disorder with impaired language and dysmorphic faciesInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- syndromic intellectual disabilityInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
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: NM_004397.6. 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 |
|---|---|---|---|---|---|---|---|---|---|
| DDX6 | NM_004397.6 | MANE Select | c.1175-5_1175-4delTT | splice_region intron | N/A | NP_004388.2 | P26196 | ||
| DDX6 | NM_001257191.3 | c.1175-5_1175-4delTT | splice_region intron | N/A | NP_001244120.1 | P26196 | |||
| DDX6 | NM_001425145.1 | c.1175-5_1175-4delTT | splice_region intron | N/A | NP_001412074.1 | P26196 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DDX6 | ENST00000534980.7 | TSL:1 MANE Select | c.1175-5_1175-4delTT | splice_region intron | N/A | ENSP00000442266.1 | P26196 | ||
| DDX6 | ENST00000526070.2 | TSL:1 | c.1175-5_1175-4delTT | splice_region intron | N/A | ENSP00000433704.1 | P26196 | ||
| DDX6 | ENST00000620157.4 | TSL:1 | c.1175-5_1175-4delTT | splice_region intron | N/A | ENSP00000478754.1 | P26196 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 146978Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
146978
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: 0.0000158 AC: 2AN: 126892 AF XY: 0.0000146 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
126892
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: 0.0000357 AC: 39AN: 1092180Hom.: 0 AF XY: 0.0000274 AC XY: 15AN XY: 546494 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
39
AN:
1092180
Hom.:
AF XY:
AC XY:
15
AN XY:
546494
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:
24624
American (AMR)
AF:
AC:
0
AN:
32230
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
18884
East Asian (EAS)
AF:
AC:
0
AN:
29398
South Asian (SAS)
AF:
AC:
0
AN:
63176
European-Finnish (FIN)
AF:
AC:
3
AN:
39646
Middle Eastern (MID)
AF:
AC:
0
AN:
4560
European-Non Finnish (NFE)
AF:
AC:
31
AN:
835400
Other (OTH)
AF:
AC:
5
AN:
44262
⚠️ 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: 0.242
Heterozygous variant carriers
0
8
16
25
33
41
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
75-80
>80
Age
GnomAD4 genome 0.00 AC: 0AN: 146978Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 71398
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
146978
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
71398
African (AFR)
AF:
AC:
0
AN:
40216
American (AMR)
AF:
AC:
0
AN:
14730
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3404
East Asian (EAS)
AF:
AC:
0
AN:
5126
South Asian (SAS)
AF:
AC:
0
AN:
4676
European-Finnish (FIN)
AF:
AC:
0
AN:
9250
Middle Eastern (MID)
AF:
AC:
0
AN:
310
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66352
Other (OTH)
AF:
AC:
0
AN:
2020
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.