Variant chr14-88575836-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_024824.5(ZC3H14):c.1023-4T>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 1,609,752 control chromosomes in the GnomAD database, including 392,062 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.59 ( 28777 hom., cov: 32)

Exomes 𝑓: 0.70 ( 363285 hom. )

Consequence

ZC3H14
NM_024824.5 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.005529

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 1.04

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 14-88575836-T-G is Benign according to our data. Variant chr14-88575836-T-G is described in ClinVar as [Benign]. Clinvar id is 130765.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZC3H14	NM_024824.5 linkuse as main transcript	c.1023-4T>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000251038.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZC3H14	ENST00000251038.10 linkuse as main transcript	c.1023-4T>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_024824.5	P3	Q6PJT7-1

Frequencies

GnomAD3 genomes

AF:

0.587

AC:

89159

AN:

151866

Hom.:

28767

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.612

Gnomad AMR

AF:

0.531

Gnomad ASJ

AF:

0.668

Gnomad EAS

AF:

0.376

Gnomad SAS

AF:

0.593

Gnomad FIN

AF:

0.791

Gnomad MID

AF:

0.627

Gnomad NFE

AF:

0.735

Gnomad OTH

AF:

0.613

GnomAD3 exomes

AF:

0.616

AC:

154469

AN:

250890

Hom.:

51011

AF XY:

0.628

AC XY:

85174

AN XY:

135670

show subpopulations

Gnomad AFR exome

AF:

0.324

Gnomad AMR exome

AF:

0.423

Gnomad ASJ exome

AF:

0.667

Gnomad EAS exome

AF:

0.344

Gnomad SAS exome

AF:

0.573

Gnomad FIN exome

AF:

0.783

Gnomad NFE exome

AF:

0.733

Gnomad OTH exome

AF:

0.654

GnomAD4 exome

AF:

0.697

AC:

1015962

AN:

1457768

Hom.:

363285

Cov.:

AF XY:

0.696

AC XY:

504765

AN XY:

725516

show subpopulations

Gnomad4 AFR exome

AF:

0.315

Gnomad4 AMR exome

AF:

0.440

Gnomad4 ASJ exome

AF:

0.672

Gnomad4 EAS exome

AF:

0.352

Gnomad4 SAS exome

AF:

0.576

Gnomad4 FIN exome

AF:

0.779

Gnomad4 NFE exome

AF:

0.740

Gnomad4 OTH exome

AF:

0.660

GnomAD4 genome

AF:

0.587

AC:

89196

AN:

151984

Hom.:

28777

Cov.:

AF XY:

0.587

AC XY:

43650

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.328

Gnomad4 AMR

AF:

0.530

Gnomad4 ASJ

AF:

0.668

Gnomad4 EAS

AF:

0.377

Gnomad4 SAS

AF:

0.595

Gnomad4 FIN

AF:

0.791

Gnomad4 NFE

AF:

0.735

Gnomad4 OTH

AF:

0.613

Alfa

AF:

0.694

Hom.:

73048

Bravo

AF:

0.552

Asia WGS

AF:

0.463

AC:

1611

AN:

3478

EpiCase

AF:

0.717

EpiControl

AF:

0.717

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, no assertion criteria provided

clinical testing

Genetic Services Laboratory, University of Chicago

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

7.5

DANN

Benign

0.64

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0055

dbscSNV1_RF

Benign

0.15

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