rs8007288

chr14-88587530-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.1280-9204A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,984 control chromosomes in the GnomAD database, including 10,487 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 0.33 (10487 hom., cov: 32)
• Consequence: ZC3H14 NM_024824.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZC3H14	NM_024824.5	c.1280-9204A>G		intron_variant		ENST00000251038.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZC3H14	ENST00000251038.10	c.1280-9204A>G		intron_variant		1	NM_024824.5	P3

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50333 AN: 151864 Hom.: 10491 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.331 AC: 50307 AN: 151984 Hom.: 10487 Cov.: 32 AF XY: 0.333 AC XY: 24704 AN XY: 74262

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.377

Alfa AF: 0.396 Hom.: 1690

Bravo AF: 0.305

Asia WGS AF: 0.141 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.3
Dann	Benign	0.42

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: rs8007288; hg19: chr14-89053874;