13-99970413-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3BS2
The NM_033132.5(ZIC5):c.1179_1190dupGCCGCCGCCGCC(p.Pro394_Pro397dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_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
Consequence
NM_033132.5 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZIC5 | NM_033132.5 | c.1179_1190dupGCCGCCGCCGCC | p.Pro394_Pro397dup | disruptive_inframe_insertion | Exon 1 of 2 | ENST00000267294.5 | NP_149123.3 | |
ZIC5 | NR_146224.1 | n.1485_1496dupGCCGCCGCCGCC | non_coding_transcript_exon_variant | Exon 1 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZIC5 | ENST00000267294.5 | c.1179_1190dupGCCGCCGCCGCC | p.Pro394_Pro397dup | disruptive_inframe_insertion | Exon 1 of 2 | 1 | NM_033132.5 | ENSP00000267294.4 | ||
ENSG00000297638 | ENST00000749511.1 | n.135+310_135+321dupGGCGGCGGCGGC | intron_variant | Intron 1 of 1 | ||||||
ENSG00000297638 | ENST00000749512.1 | n.104+304_104+315dupGGCGGCGGCGGC | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.000238 AC: 29AN: 121980Hom.: 0 Cov.: 0 show subpopulations
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000155 AC: 153AN: 984558Hom.: 0 Cov.: 5 AF XY: 0.000171 AC XY: 81AN XY: 472570 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome AF: 0.000238 AC: 29AN: 122080Hom.: 0 Cov.: 0 AF XY: 0.000251 AC XY: 15AN XY: 59662 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at