rs748325646
Your query was ambiguous. Multiple possible variants found:
- chrX-137566825-ACGCCGCCGCCGCCGC-A
- chrX-137566825-ACGCCGCCGCCGCCGC-ACGC
- chrX-137566825-ACGCCGCCGCCGCCGC-ACGCCGC
- chrX-137566825-ACGCCGCCGCCGCCGC-ACGCCGCCGC
- chrX-137566825-ACGCCGCCGCCGCCGC-ACGCCGCCGCCGC
- chrX-137566825-ACGCCGCCGCCGCCGC-ACGCCGCCGCCGCCGCCGC
- chrX-137566825-ACGCCGCCGCCGCCGC-ACGCCGCCGCCGCCGCCGCCGC
- chrX-137566825-ACGCCGCCGCCGCCGC-ACGCCGCCGCCGCCGCCGCCGCCGC
- chrX-137566825-ACGCCGCCGCCGCCGC-ACGCCGCCGCCGCCGCCGCCGCCGCCGC
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3BS2
The NM_003413.4(ZIC3):c.147_161delCGCCGCCGCCGCCGC(p.Ala50_Ala54del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,160,637 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. 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 0.000027 ( 0 hom., 2 hem., cov: 24)
Exomes 𝑓: 0.000012 ( 0 hom. 2 hem. )
Consequence
ZIC3
NM_003413.4 disruptive_inframe_deletion
NM_003413.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.41
Publications
0 publications found
Genes affected
ZIC3 (HGNC:12874): (Zic family member 3) This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. This nuclear protein probably functions as a transcription factor in early stages of left-right body axis formation. Mutations in this gene cause X-linked visceral heterotaxy, which includes congenital heart disease and left-right axis defects in organs. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_003413.4
BS2
High Hemizygotes in GnomAd4 at 2 XL gene
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ZIC3 | NM_003413.4 | c.147_161delCGCCGCCGCCGCCGC | p.Ala50_Ala54del | disruptive_inframe_deletion | Exon 1 of 3 | ENST00000287538.10 | NP_003404.1 | |
| ZIC3 | NM_001330661.1 | c.147_161delCGCCGCCGCCGCCGC | p.Ala50_Ala54del | disruptive_inframe_deletion | Exon 1 of 3 | NP_001317590.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ZIC3 | ENST00000287538.10 | c.147_161delCGCCGCCGCCGCCGC | p.Ala50_Ala54del | disruptive_inframe_deletion | Exon 1 of 3 | 1 | NM_003413.4 | ENSP00000287538.5 | ||
| ZIC3 | ENST00000370606.3 | c.147_161delCGCCGCCGCCGCCGC | p.Ala50_Ala54del | disruptive_inframe_deletion | Exon 1 of 3 | 5 | ENSP00000359638.3 | |||
| LINC02931 | ENST00000786828.1 | n.130+2234_130+2248delGCGGCGGCGGCGGCG | intron_variant | Intron 1 of 5 |
Frequencies
GnomAD3 genomes 0.0000268 AC: 3AN: 111760Hom.: 0 Cov.: 24 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
111760
Hom.:
Cov.:
24
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: 0.0000124 AC: 13AN: 1048877Hom.: 0 AF XY: 0.00000586 AC XY: 2AN XY: 341519 show subpopulations
GnomAD4 exome
AF:
AC:
13
AN:
1048877
Hom.:
AF XY:
AC XY:
2
AN XY:
341519
show subpopulations
African (AFR)
AF:
AC:
0
AN:
25002
American (AMR)
AF:
AC:
0
AN:
28191
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
18644
East Asian (EAS)
AF:
AC:
0
AN:
27323
South Asian (SAS)
AF:
AC:
0
AN:
49919
European-Finnish (FIN)
AF:
AC:
0
AN:
31347
Middle Eastern (MID)
AF:
AC:
0
AN:
3940
European-Non Finnish (NFE)
AF:
AC:
11
AN:
820182
Other (OTH)
AF:
AC:
2
AN:
44329
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.430
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000268 AC: 3AN: 111760Hom.: 0 Cov.: 24 AF XY: 0.0000586 AC XY: 2AN XY: 34146 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
111760
Hom.:
Cov.:
24
AF XY:
AC XY:
2
AN XY:
34146
show subpopulations
African (AFR)
AF:
AC:
0
AN:
30859
American (AMR)
AF:
AC:
0
AN:
10712
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2640
East Asian (EAS)
AF:
AC:
0
AN:
3508
South Asian (SAS)
AF:
AC:
0
AN:
2697
European-Finnish (FIN)
AF:
AC:
0
AN:
6008
Middle Eastern (MID)
AF:
AC:
0
AN:
237
European-Non Finnish (NFE)
AF:
AC:
3
AN:
52921
Other (OTH)
AF:
AC:
0
AN:
1499
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
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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