14-88620934-TAAAAAA-TAAAAA

Variant names:

• chr14-88620934-TA-T
• rs35953031
• NM_024824.5:c.*9200delA

Variant summary

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

The NM_024824.5(ZC3H14):​c.*9200delA variant causes a 3 prime UTR 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 0.0056 (3 hom., cov: 0)
  • Exomes 𝑓: 0.16 (1 hom.)
• Consequence: ZC3H14 NM_024824.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

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]

EML5 (HGNC:18197): (EMAP like 5) Predicted to enable microtubule binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZC3H14	NM_024824.5	c.*9200delA		3_prime_UTR_variant	Exon 17 of 17	ENST00000251038.10	NP_079100.2
EML5	NM_183387.3	c.5203-9delT		intron_variant	Intron 38 of 43	ENST00000554922.6	NP_899243.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZC3H14	ENST00000251038.10	c.*9200delA		3_prime_UTR_variant	Exon 17 of 17	1	NM_024824.5	ENSP00000251038.5
EML5	ENST00000554922.6	c.5203-9delT		intron_variant	Intron 38 of 43	5	NM_183387.3	ENSP00000451998.1

Frequencies

GnomAD3 genomes AF: 0.00555 AC: 771 AN: 138808 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00391

Gnomad ASJ AF: 0.00119

Gnomad EAS AF: 0.00396

Gnomad SAS AF: 0.00116

Gnomad FIN AF: 0.0122

Gnomad MID AF: 0.00352

Gnomad NFE AF: 0.00262

Gnomad OTH AF: 0.00535

GnomAD3 exomes AF: 0.250 AC: 13084 AN: 52316 Hom.: 1 AF XY: 0.251 AC XY: 6619 AN XY: 26334

Gnomad AFR exome AF: 0.275

Gnomad AMR exome AF: 0.232

Gnomad ASJ exome AF: 0.259

Gnomad EAS exome AF: 0.276

Gnomad SAS exome AF: 0.267

Gnomad FIN exome AF: 0.229

Gnomad NFE exome AF: 0.246

Gnomad OTH exome AF: 0.231

GnomAD4 exome AF: 0.164 AC: 188385 AN: 1148772 Hom.: 1 Cov.: 0 AF XY: 0.166 AC XY: 93181 AN XY: 560256

Gnomad4 AFR exome AF: 0.212

Gnomad4 AMR exome AF: 0.186

Gnomad4 ASJ exome AF: 0.166

Gnomad4 EAS exome AF: 0.226

Gnomad4 SAS exome AF: 0.217

Gnomad4 FIN exome AF: 0.178

Gnomad4 NFE exome AF: 0.156

Gnomad4 OTH exome AF: 0.176

GnomAD4 genome AF: 0.00560 AC: 777 AN: 138816 Hom.: 3 Cov.: 0 AF XY: 0.00610 AC XY: 407 AN XY: 66668

Gnomad4 AFR AF: 0.0113

Gnomad4 AMR AF: 0.00390

Gnomad4 ASJ AF: 0.00119

Gnomad4 EAS AF: 0.00398

Gnomad4 SAS AF: 0.00140

Gnomad4 FIN AF: 0.0122

Gnomad4 NFE AF: 0.00262

Gnomad4 OTH AF: 0.00534

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs35953031; hg19: chr14-89087278;