rs10682918

chr14-88571138-C-CAchr14-88571138-C-CATchr14-88571138-C-CATTchr14-88571138-C-CATTTchr14-88571138-C-CATTTTTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_024824.5(ZC3H14):c.235+14_235+15insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 1,397,666 control chromosomes in the GnomAD database, including 15 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00013 (0 hom., cov: 0)
  • Exomes 𝑓: 0.013 (15 hom.)
• Consequence: ZC3H14 NM_024824.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZC3H14	NM_024824.5	c.235+14_235+15insA		intron_variant		ENST00000251038.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZC3H14	ENST00000251038.10	c.235+14_235+15insA		intron_variant		1	NM_024824.5	P3

Frequencies

GnomAD3 genomes AF: 0.000133 AC: 20 AN: 150674 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000132

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00127

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0000443

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0118 AC: 2285 AN: 193698 Hom.: 2 AF XY: 0.0118 AC XY: 1235 AN XY: 104448

Gnomad AFR exome AF: 0.00335

Gnomad AMR exome AF: 0.00952

Gnomad ASJ exome AF: 0.0158

Gnomad EAS exome AF: 0.00796

Gnomad SAS exome AF: 0.0142

Gnomad FIN exome AF: 0.00503

Gnomad NFE exome AF: 0.0146

Gnomad OTH exome AF: 0.0166

GnomAD4 exome AF: 0.0126 AC: 15711 AN: 1246888 Hom.: 15 Cov.: 18 AF XY: 0.0124 AC XY: 7665 AN XY: 619498

Gnomad4 AFR exome AF: 0.00466

Gnomad4 AMR exome AF: 0.00830

Gnomad4 ASJ exome AF: 0.0130

Gnomad4 EAS exome AF: 0.00408

Gnomad4 SAS exome AF: 0.0152

Gnomad4 FIN exome AF: 0.0115

Gnomad4 NFE exome AF: 0.0133

Gnomad4 OTH exome AF: 0.0120

GnomAD4 genome AF: 0.000133 AC: 20 AN: 150778 Hom.: 0 Cov.: 0 AF XY: 0.0000951 AC XY: 7 AN XY: 73624

Gnomad4 AFR AF: 0.0000244

Gnomad4 AMR AF: 0.000132

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00127

Gnomad4 NFE AF: 0.0000443

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0393 Hom.: 2617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs10682918; hg19: chr14-89037482;