X-137566825-ACGCCGCCGCCGCCGC-ACGCCGCCGCCGCCGCCGCCGCCGCCGC
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP3
The NM_003413.4(ZIC3):c.150_161dup(p.Ala52_Ala55dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000517 in 1,160,682 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 1 hem., cov: 24)
Exomes 𝑓: 0.0000038 ( 0 hom. 1 hem. )
Consequence
ZIC3
NM_003413.4 inframe_insertion
NM_003413.4 inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.41
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 made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP3
?
Nonframeshift variant in repetitive region in NM_003413.4
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZIC3 | NM_003413.4 | c.150_161dup | p.Ala52_Ala55dup | inframe_insertion | 1/3 | ENST00000287538.10 | |
ZIC3 | NM_001330661.1 | c.150_161dup | p.Ala52_Ala55dup | inframe_insertion | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZIC3 | ENST00000287538.10 | c.150_161dup | p.Ala52_Ala55dup | inframe_insertion | 1/3 | 1 | NM_003413.4 | P1 | |
ZIC3 | ENST00000370606.3 | c.150_161dup | p.Ala52_Ala55dup | inframe_insertion | 1/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111761Hom.: 0 Cov.: 24 AF XY: 0.0000293 AC XY: 1AN XY: 34147
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GnomAD4 exome AF: 0.00000381 AC: 4AN: 1048878Hom.: 0 Cov.: 33 AF XY: 0.00000293 AC XY: 1AN XY: 341520
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GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111804Hom.: 0 Cov.: 24 AF XY: 0.0000292 AC XY: 1AN XY: 34200
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at