Variant chr14-88620934-T-TAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_024824.5(ZC3H14):c.*9198_*9200dupAAA variant causes a 3 prime UTR 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 0.000079 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00014 ( 0 hom. )

Consequence

ZC3H14
NM_024824.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.252

Variant links:

Genes affected

ZC3H14 (HGNC:20509): (zinc finger CCCH-type containing 14) The protein encoded by this gene is a poly(A)-binding protein that can affect gene expression and poly(A) tail length. The encoded protein may influence mRNA stability, nuclear export, and translation. [provided by RefSeq, May 2016]

ZC3H14 links:

EML5 (HGNC:18197): (EMAP like 5) Predicted to enable microtubule binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

EML5 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZC3H14	NM_024824.5 link	c.9198_9200dupAAA		3_prime_UTR_variant	17/17	ENST00000251038.10	NP_079100.2	Q6PJT7-1
EML5	NM_183387.3 link	c.5203-11_5203-9dupTTT		intron_variant		ENST00000554922.6	NP_899243.1	Q05BV3-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZC3H14	ENST00000251038.10 link	c.9198_9200dupAAA		3_prime_UTR_variant	17/17	1	NM_024824.5	ENSP00000251038.5		Q6PJT7-1
EML5	ENST00000554922.6 link	c.5203-11_5203-9dupTTT		intron_variant		5	NM_183387.3	ENSP00000451998.1		Q05BV3-5

Frequencies

GnomAD3 genomes

AF:

0.0000792

AC:

AN:

138868

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000134

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000233

Gnomad FIN

AF:

0.000135

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000463

Gnomad OTH

AF:

0.000535

GnomAD4 exome

AF:

0.000141

AC:

174

AN:

1233174

Hom.:

Cov.:

AF XY:

0.000153

AC XY:

AN XY:

600996

show subpopulations

Gnomad4 AFR exome

AF:

0.000447

Gnomad4 AMR exome

AF:

0.000592

Gnomad4 ASJ exome

AF:

0.000108

Gnomad4 EAS exome

AF:

0.000212

Gnomad4 SAS exome

AF:

0.000448

Gnomad4 FIN exome

AF:

0.000109

Gnomad4 NFE exome

AF:

0.000109

Gnomad4 OTH exome

AF:

0.0000979

GnomAD4 genome

AF:

0.0000792

AC:

AN:

138876

Hom.:

Cov.:

AF XY:

0.0000450

AC XY:

AN XY:

66712

show subpopulations

Gnomad4 AFR

AF:

0.000134

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000234

Gnomad4 FIN

AF:

0.000135

Gnomad4 NFE

AF:

0.0000463

Gnomad4 OTH

AF:

0.000534

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