Variant 13-99970413-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGC 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_1190del(p.Pro399_Pro400del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000784 in 1,098,634 control chromosomes in the GnomAD database, including 6 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0010 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00075 ( 6 hom. )

Consequence

ZIC5
NM_033132.5 inframe_deletion

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 125 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZIC5	NM_033132.5 linkuse as main transcript	c.1185_1190del	p.Pro399_Pro400del	inframe_deletion	1/2	ENST00000267294.5
ZIC5	NR_146224.1 linkuse as main transcript	n.1491_1496del		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZIC5	ENST00000267294.5 linkuse as main transcript	c.1185_1190del	p.Pro399_Pro400del	inframe_deletion	1/2	1	NM_033132.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00103

AC:

126

AN:

121976

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000860

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000278

Gnomad SAS

AF:

0.000275

Gnomad FIN

AF:

0.00615

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000584

Gnomad OTH

AF:

0.000613

GnomAD4 exome

AF:

0.000754

AC:

736

AN:

976558

Hom.:

AF XY:

0.000841

AC XY:

394

AN XY:

468758

show subpopulations

Gnomad4 AFR exome

AF:

0.00259

Gnomad4 AMR exome

AF:

0.00157

Gnomad4 ASJ exome

AF:

0.000437

Gnomad4 EAS exome

AF:

0.000833

Gnomad4 SAS exome

AF:

0.000781

Gnomad4 FIN exome

AF:

0.00380

Gnomad4 NFE exome

AF:

0.000662

Gnomad4 OTH exome

AF:

0.000756

GnomAD4 genome

AF:

0.00102

AC:

125

AN:

122076

Hom.:

Cov.:

AF XY:

0.00119

AC XY:

AN XY:

59658

show subpopulations

Gnomad4 AFR

AF:

0.00113

Gnomad4 AMR

AF:

0.000858

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000279

Gnomad4 SAS

AF:

0.000277

Gnomad4 FIN

AF:

0.00615

Gnomad4 NFE

AF:

0.000584

Gnomad4 OTH

AF:

0.000608

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