chr14-88571138-C-CATT

Position:

• chr14-88571138-C-CATT

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_024824.5(ZC3H14):​c.235+14_235+15insATT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00027 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0050 (3 hom.)
• Consequence: ZC3H14 NM_024824.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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 -6 ACMG points.

• BP6: Variant 14-88571138-C-CATT is Benign according to our data. Variant chr14-88571138-C-CATT is described in ClinVar as [Likely_benign]. Clinvar id is 445396.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.000265 AC: 40 AN: 150722 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000587

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000194

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000207

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00279 AC: 541 AN: 193698 Hom.: 0 AF XY: 0.00273 AC XY: 285 AN XY: 104448

Gnomad AFR exome AF: 0.00224

Gnomad AMR exome AF: 0.00355

Gnomad ASJ exome AF: 0.00387

Gnomad EAS exome AF: 0.00168

Gnomad SAS exome AF: 0.00310

Gnomad FIN exome AF: 0.000995

Gnomad NFE exome AF: 0.00303

Gnomad OTH exome AF: 0.00306

GnomAD4 exome AF: 0.00503 AC: 6450 AN: 1283300 Hom.: 3 Cov.: 18 AF XY: 0.00485 AC XY: 3098 AN XY: 638518

Gnomad4 AFR exome AF: 0.00197

Gnomad4 AMR exome AF: 0.00310

Gnomad4 ASJ exome AF: 0.00449

Gnomad4 EAS exome AF: 0.00109

Gnomad4 SAS exome AF: 0.00557

Gnomad4 FIN exome AF: 0.00397

Gnomad4 NFE exome AF: 0.00542

Gnomad4 OTH exome AF: 0.00435

GnomAD4 genome AF: 0.000265 AC: 40 AN: 150826 Hom.: 0 Cov.: 0 AF XY: 0.000217 AC XY: 16 AN XY: 73662

Gnomad4 AFR AF: 0.000585

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000194

Gnomad4 NFE AF: 0.000207

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0114 Hom.: 2617

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Aug 31, 2017

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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;