14-88620934-TAAAAAA-TAAAA

Variant names:

• chr14-88620934-TAA-T
• rs35953031
• NM_024824.5:c.*9199_*9200delAA

Variant summary

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

The NM_024824.5(ZC3H14):​c.*9199_*9200delAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 1,320,434 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00044 (0 hom., cov: 0)
  • Exomes 𝑓: 0.022 (0 hom.)
• Consequence: ZC3H14 NM_024824.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.826

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 (SAS) allele frequency at 95% confidence interval = 0.0513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZC3H14	NM_024824.5	c.*9199_*9200delAA		3_prime_UTR_variant	Exon 17 of 17	ENST00000251038.10	NP_079100.2
EML5	NM_183387.3	c.5203-10_5203-9delTT		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.*9199_*9200delAA		3_prime_UTR_variant	Exon 17 of 17	1	NM_024824.5	ENSP00000251038.5
EML5	ENST00000554922.6	c.5203-10_5203-9delTT		intron_variant	Intron 38 of 43	5	NM_183387.3	ENSP00000451998.1

Frequencies

GnomAD3 genomes AF: 0.000440 AC: 61 AN: 138782 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000295

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000435

Gnomad ASJ AF: 0.000594

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00218

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000401

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0623 AC: 3258 AN: 52316 Hom.: 0 AF XY: 0.0677 AC XY: 1784 AN XY: 26334

Gnomad AFR exome AF: 0.0715

Gnomad AMR exome AF: 0.0760

Gnomad ASJ exome AF: 0.0606

Gnomad EAS exome AF: 0.0850

Gnomad SAS exome AF: 0.0968

Gnomad FIN exome AF: 0.0237

Gnomad NFE exome AF: 0.0550

Gnomad OTH exome AF: 0.0543

GnomAD4 exome AF: 0.0218 AC: 25805 AN: 1181652 Hom.: 0 AF XY: 0.0230 AC XY: 13257 AN XY: 575540

Gnomad4 AFR exome AF: 0.0329

Gnomad4 AMR exome AF: 0.0402

Gnomad4 ASJ exome AF: 0.0214

Gnomad4 EAS exome AF: 0.0329

Gnomad4 SAS exome AF: 0.0529

Gnomad4 FIN exome AF: 0.0222

Gnomad4 NFE exome AF: 0.0191

Gnomad4 OTH exome AF: 0.0219

GnomAD4 genome AF: 0.000440 AC: 61 AN: 138782 Hom.: 0 Cov.: 0 AF XY: 0.000465 AC XY: 31 AN XY: 66616

Gnomad4 AFR AF: 0.000295

Gnomad4 AMR AF: 0.000435

Gnomad4 ASJ AF: 0.000594

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00218

Gnomad4 NFE AF: 0.000401

Gnomad4 OTH AF: 0.00

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;