Variant chr13-99970413-T-TGGCGGCGGC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2

The NM_033132.5(ZIC5):c.1190_1191insGCCGCCGCC(p.Pro398_Pro400dup) variant causes a 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 0.0015 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00098 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ZIC5
NM_033132.5 inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.56

Variant links:

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]

ZIC5 links:

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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 180 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZIC5	NM_033132.5 linkuse as main transcript	c.1190_1191insGCCGCCGCC	p.Pro398_Pro400dup	inframe_insertion	1/2	ENST00000267294.5	NP_149123.3
ZIC5	NR_146224.1 linkuse as main transcript	n.1496_1497insGCCGCCGCC		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZIC5	ENST00000267294.5 linkuse as main transcript	c.1190_1191insGCCGCCGCC	p.Pro398_Pro400dup	inframe_insertion	1/2	1	NM_033132.5	ENSP00000267294	P1

Frequencies

GnomAD3 genomes

AF:

0.00148

AC:

180

AN:

121980

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000847

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00273

Gnomad ASJ

AF:

0.00742

Gnomad EAS

AF:

0.00139

Gnomad SAS

AF:

0.00110

Gnomad FIN

AF:

0.000158

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00148

Gnomad OTH

AF:

0.00123

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000983

AC:

968

AN:

984536

Hom.:

Cov.:

AF XY:

0.000912

AC XY:

431

AN XY:

472562

show subpopulations

Gnomad4 AFR exome

AF:

0.000669

Gnomad4 AMR exome

AF:

0.000311

Gnomad4 ASJ exome

AF:

0.00296

Gnomad4 EAS exome

AF:

0.000346

Gnomad4 SAS exome

AF:

0.000936

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000975

Gnomad4 OTH exome

AF:

0.00158

GnomAD4 genome

AF:

0.00147

AC:

180

AN:

122080

Hom.:

Cov.:

AF XY:

0.00129

AC XY:

AN XY:

59662

show subpopulations

Gnomad4 AFR

AF:

0.000845

Gnomad4 AMR

AF:

0.00273

Gnomad4 ASJ

AF:

0.00742

Gnomad4 EAS

AF:

0.00139

Gnomad4 SAS

AF:

0.00111

Gnomad4 FIN

AF:

0.000158

Gnomad4 NFE

AF:

0.00148

Gnomad4 OTH

AF:

0.00122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over