rs187183577
Variant names:
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_005675.6(DGCR6):c.24G>A(p.Leu8Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.034 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
DGCR6
NM_005675.6 synonymous
NM_005675.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.232
Publications
0 publications found
Genes affected
DGCR6 (HGNC:2846): (DiGeorge syndrome critical region gene 6) DiGeorge syndrome, and more widely, the CATCH 22 syndrome, are associated with microdeletions in chromosomal region 22q11.2. The product of this gene shares homology with the Drosophila melanogaster gonadal protein, which participates in gonadal and germ cell development, and with the gamma-1 subunit of human laminin. This gene is a candidate for involvement in DiGeorge syndrome pathology and in schizophrenia. [provided by RefSeq, Nov 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
Variant 22-18906398-G-A is Benign according to our data. Variant chr22-18906398-G-A is described in ClinVar as Benign. ClinVar VariationId is 779194.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.232 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005675.6. 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 |
|---|---|---|---|---|---|---|---|---|---|
| DGCR6 | NM_005675.6 | MANE Select | c.24G>A | p.Leu8Leu | synonymous | Exon 1 of 5 | NP_005666.2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DGCR6 | ENST00000331444.12 | TSL:1 MANE Select | c.24G>A | p.Leu8Leu | synonymous | Exon 1 of 5 | ENSP00000331681.6 | Q14129-1 | |
| ENSG00000283809 | ENST00000638240.1 | TSL:5 | c.24G>A | p.Leu8Leu | synonymous | Exon 1 of 6 | ENSP00000492446.1 | A0A1W2PRQ8 | |
| DGCR6 | ENST00000413981.5 | TSL:1 | c.-298-167G>A | intron | N/A | ENSP00000402409.1 | Q6FGH4 |
Frequencies
GnomAD3 genomes 0 Cov.: 0
GnomAD3 genomes
AC:
0
AN:
0
Hom.:
Cov.:
0
GnomAD2 exomes AF: 0.00639 AC: 1344AN: 210330 AF XY: 0.00464 show subpopulations
GnomAD2 exomes
AF:
AC:
1344
AN:
210330
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 Data not reliable, filtered out with message: AS_VQSR AF: 0.0339 AC: 4AN: 118Hom.: 1 Cov.: 0 AF XY: 0.0395 AC XY: 3AN XY: 76 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
4
AN:
118
Hom.:
Cov.:
0
AF XY:
AC XY:
3
AN XY:
76
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
4
AN:
22
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2
East Asian (EAS)
AF:
AC:
0
AN:
8
South Asian (SAS)
AF:
AC:
0
AN:
40
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
44
Other (OTH)
AF:
AC:
0
AN:
2
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
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 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
4
AN:
3474
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Benign
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
-
2
not provided (2)
Computational 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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.