Variant 13-99970413-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC 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.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

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 623 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZIC5	NM_033132.5 link	c.1185_1190dupGCCGCC	p.Pro396_Pro397dup	disruptive_inframe_insertion	1/2	ENST00000267294.5	NP_149123.3	Q96T25
ZIC5	NR_146224.1 link	n.1491_1496dupGCCGCC		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZIC5	ENST00000267294.5 link	c.1185_1190dupGCCGCC	p.Pro396_Pro397dup	disruptive_inframe_insertion	1/2	1	NM_033132.5	ENSP00000267294.4		Q96T25

Frequencies

GnomAD3 genomes

AF:

0.00508

AC:

620

AN:

121974

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00421

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00563

Gnomad ASJ

AF:

0.00574

Gnomad EAS

AF:

0.0131

Gnomad SAS

AF:

0.00771

Gnomad FIN

AF:

0.00189

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00531

Gnomad OTH

AF:

0.00245

GnomAD4 exome

AF:

0.00385

AC:

3795

AN:

984506

Hom.:

Cov.:

AF XY:

0.00378

AC XY:

1785

AN XY:

472538

show subpopulations

Gnomad4 AFR exome

AF:

0.00363

Gnomad4 AMR exome

AF:

0.000779

Gnomad4 ASJ exome

AF:

0.00174

Gnomad4 EAS exome

AF:

0.00249

Gnomad4 SAS exome

AF:

0.00345

Gnomad4 FIN exome

AF:

0.0000772

Gnomad4 NFE exome

AF:

0.00403

Gnomad4 OTH exome

AF:

0.00328

GnomAD4 genome

AF:

0.00510

AC:

623

AN:

122074

Hom.:

Cov.:

AF XY:

0.00479

AC XY:

286

AN XY:

59656

show subpopulations

Gnomad4 AFR

AF:

0.00425

Gnomad4 AMR

AF:

0.00561

Gnomad4 ASJ

AF:

0.00574

Gnomad4 EAS

AF:

0.0131

Gnomad4 SAS

AF:

0.00774

Gnomad4 FIN

AF:

0.00189

Gnomad4 NFE

AF:

0.00531

Gnomad4 OTH

AF:

0.00304

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