13-99970413-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_033132.5(ZIC5):c.1185_1190dupGCCGCC(p.Pro396_Pro397dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0051 ( 4 hom., cov: 0)
Exomes 𝑓: 0.0039 ( 5 hom. )
Consequence
ZIC5
NM_033132.5 disruptive_inframe_insertion
NM_033132.5 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.56
Genes affected
ZIC5 (HGNC:20322): (Zic family member 5) This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. The encoded protein may act as a transcriptional repressor. Studies in mouse and Xenopus support a role for this gene in neural crest development. Elevated expression of this gene has been observed in various human cancers and may contribute to cancer progression. This gene is closely linked to a related family member on chromosome 13. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_033132.5
BS2
High AC in GnomAd4 at 623 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00508 AC: 620AN: 121974Hom.: 4 Cov.: 0
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GnomAD4 exome AF: 0.00385 AC: 3795AN: 984506Hom.: 5 Cov.: 5 AF XY: 0.00378 AC XY: 1785AN XY: 472538
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GnomAD4 genome AF: 0.00510 AC: 623AN: 122074Hom.: 4 Cov.: 0 AF XY: 0.00479 AC XY: 286AN XY: 59656
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ClinVar
Not reported inComputational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at