rs11159862

Positions:

• chr14-88597933-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024824.5(ZC3H14):​c.1354+1125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,150 control chromosomes in the GnomAD database, including 3,153 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (3153 hom., cov: 32)
• Consequence: ZC3H14 NM_024824.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZC3H14	NM_024824.5	c.1354+1125A>G		intron_variant		ENST00000251038.10	NP_079100.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZC3H14	ENST00000251038.10	c.1354+1125A>G		intron_variant		1	NM_024824.5	ENSP00000251038.5

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28177 AN: 152032 Hom.: 3146 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.208

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.185 AC: 28212 AN: 152150 Hom.: 3153 Cov.: 32 AF XY: 0.191 AC XY: 14181 AN XY: 74356

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.210

Alfa AF: 0.169 Hom.: 351

Bravo AF: 0.205

Asia WGS AF: 0.346 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.54

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

Other links and lift over

dbSNP: rs11159862; hg19: chr14-89064277;