Variant 14-88596823-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_024824.5(ZC3H14):c.1354+15A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 1,611,292 control chromosomes in the GnomAD database, including 606,639 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.85 ( 55510 hom., cov: 31)

Exomes 𝑓: 0.87 ( 551129 hom. )

Consequence

ZC3H14
NM_024824.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.822

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:

ZC3H14 (HGNC:):

ZC3H14 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 14-88596823-A-G is Benign according to our data. Variant chr14-88596823-A-G is described in ClinVar as [Benign]. Clinvar id is 1684249.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZC3H14	NM_024824.5 linkuse as main transcript	c.1354+15A>G		intron_variant		ENST00000251038.10	NP_079100.2	Q6PJT7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZC3H14	ENST00000251038.10 linkuse as main transcript	c.1354+15A>G		intron_variant		1	NM_024824.5	ENSP00000251038.5		Q6PJT7-1

Frequencies

GnomAD3 genomes

AF:

0.852

AC:

129557

AN:

152014

Hom.:

55454

Cov.:

show subpopulations

Gnomad AFR

AF:

0.773

Gnomad AMI

AF:

0.840

Gnomad AMR

AF:

0.910

Gnomad ASJ

AF:

0.916

Gnomad EAS

AF:

0.924

Gnomad SAS

AF:

0.767

Gnomad FIN

AF:

0.907

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.875

Gnomad OTH

AF:

0.880

GnomAD3 exomes

AF:

0.871

AC:

218848

AN:

251158

Hom.:

95809

AF XY:

0.864

AC XY:

117326

AN XY:

135736

show subpopulations

Gnomad AFR exome

AF:

0.776

Gnomad AMR exome

AF:

0.945

Gnomad ASJ exome

AF:

0.914

Gnomad EAS exome

AF:

0.918

Gnomad SAS exome

AF:

0.748

Gnomad FIN exome

AF:

0.900

Gnomad NFE exome

AF:

0.878

Gnomad OTH exome

AF:

0.881

GnomAD4 exome

AF:

0.868

AC:

1266563

AN:

1459160

Hom.:

551129

Cov.:

AF XY:

0.865

AC XY:

628092

AN XY:

726090

show subpopulations

Gnomad4 AFR exome

AF:

0.771

Gnomad4 AMR exome

AF:

0.942

Gnomad4 ASJ exome

AF:

0.916

Gnomad4 EAS exome

AF:

0.942

Gnomad4 SAS exome

AF:

0.749

Gnomad4 FIN exome

AF:

0.899

Gnomad4 NFE exome

AF:

0.872

Gnomad4 OTH exome

AF:

0.864

GnomAD4 genome

AF:

0.852

AC:

129670

AN:

152132

Hom.:

55510

Cov.:

AF XY:

0.854

AC XY:

63508

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.773

Gnomad4 AMR

AF:

0.910

Gnomad4 ASJ

AF:

0.916

Gnomad4 EAS

AF:

0.924

Gnomad4 SAS

AF:

0.768

Gnomad4 FIN

AF:

0.907

Gnomad4 NFE

AF:

0.875

Gnomad4 OTH

AF:

0.881

Alfa

AF:

0.879

Hom.:

10496

Bravo

AF:

0.854

Asia WGS

AF:

0.858

AC:

2987

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Intellectual disability, autosomal recessive 56

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.073

DANN

Benign

0.28

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over