Genetic Variant NM_024824.5:c.235+14_235+15insAT (chr14-88571138-C-CAT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_024824.5(ZC3H14):c.235+14_235+15insAT variant causes a intron 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 0.61 ( 29929 hom., cov: 0)

Exomes 𝑓: 0.63 ( 235987 hom. )

Consequence

ZC3H14
NM_024824.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.33

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

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 rank	MANE	Protein	UniProt
ZC3H14	NM_024824.5 link	c.235+14_235+15insAT		intron_variant	Intron 4 of 16	ENST00000251038.10	NP_079100.2	Q6PJT7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZC3H14	ENST00000251038.10 link	c.235+14_235+15insAT		intron_variant	Intron 4 of 16	1	NM_024824.5	ENSP00000251038.5		Q6PJT7-1

Frequencies

GnomAD3 genomes

AF:

0.614

AC:

92450

AN:

150630

Hom.:

29915

Cov.:

show subpopulations

Gnomad AFR

AF:

0.418

Gnomad AMI

AF:

0.611

Gnomad AMR

AF:

0.545

Gnomad ASJ

AF:

0.667

Gnomad EAS

AF:

0.399

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.786

Gnomad MID

AF:

0.624

Gnomad NFE

AF:

0.735

Gnomad OTH

AF:

0.635

GnomAD3 exomes

AF:

0.581

AC:

112470

AN:

193698

Hom.:

30771

AF XY:

0.587

AC XY:

61308

AN XY:

104448

show subpopulations

Gnomad AFR exome

AF:

0.409

Gnomad AMR exome

AF:

0.411

Gnomad ASJ exome

AF:

0.586

Gnomad EAS exome

AF:

0.376

Gnomad SAS exome

AF:

0.512

Gnomad FIN exome

AF:

0.747

Gnomad NFE exome

AF:

0.672

Gnomad OTH exome

AF:

0.604

GnomAD4 exome

AF:

0.627

AC:

814885

AN:

1299342

Hom.:

235987

Cov.:

AF XY:

0.625

AC XY:

404384

AN XY:

646830

show subpopulations

Gnomad4 AFR exome

AF:

0.371

Gnomad4 AMR exome

AF:

0.402

Gnomad4 ASJ exome

AF:

0.595

Gnomad4 EAS exome

AF:

0.351

Gnomad4 SAS exome

AF:

0.502

Gnomad4 FIN exome

AF:

0.709

Gnomad4 NFE exome

AF:

0.662

Gnomad4 OTH exome

AF:

0.596

GnomAD4 genome

AF:

0.614

AC:

92493

AN:

150734

Hom.:

29929

Cov.:

AF XY:

0.613

AC XY:

45117

AN XY:

73610

show subpopulations

Gnomad4 AFR

AF:

0.418

Gnomad4 AMR

AF:

0.545

Gnomad4 ASJ

AF:

0.667

Gnomad4 EAS

AF:

0.400

Gnomad4 SAS

AF:

0.597

Gnomad4 FIN

AF:

0.786

Gnomad4 NFE

AF:

0.735

Gnomad4 OTH

AF:

0.635

Alfa

AF:

0.562

Hom.:

2617

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