14-88620934-TAAAAAA-TAAAAAAAA

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_024824.5(ZC3H14):​c.*9199_*9200dupAA 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 0.013 (22 hom., cov: 0)
  • Exomes 𝑓: 0.0056 (0 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.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0132 (1835/138866) while in subpopulation AFR AF= 0.0351 (1311/37398). AF 95% confidence interval is 0.0335. There are 22 homozygotes in gnomad4. There are 811 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 22 AR gene

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0132 AC: 1833 AN: 138858 Hom.: 22 Cov.: 0

Gnomad AFR AF: 0.0351

Gnomad AMI AF: 0.00450

Gnomad AMR AF: 0.00905

Gnomad ASJ AF: 0.0146

Gnomad EAS AF: 0.00167

Gnomad SAS AF: 0.00233

Gnomad FIN AF: 0.00285

Gnomad MID AF: 0.00704

Gnomad NFE AF: 0.00441

Gnomad OTH AF: 0.0102

GnomAD3 exomes AF: 0.0114 AC: 597 AN: 52316 Hom.: 0 AF XY: 0.0113 AC XY: 298 AN XY: 26334

Gnomad AFR exome AF: 0.0241

Gnomad AMR exome AF: 0.0143

Gnomad ASJ exome AF: 0.00680

Gnomad EAS exome AF: 0.00840

Gnomad SAS exome AF: 0.00815

Gnomad FIN exome AF: 0.00996

Gnomad NFE exome AF: 0.0102

Gnomad OTH exome AF: 0.0169

GnomAD4 exome AF: 0.00557 AC: 6853 AN: 1229610 Hom.: 0 Cov.: 0 AF XY: 0.00553 AC XY: 3315 AN XY: 599252

Gnomad4 AFR exome AF: 0.0195

Gnomad4 AMR exome AF: 0.00903

Gnomad4 ASJ exome AF: 0.0108

Gnomad4 EAS exome AF: 0.00297

Gnomad4 SAS exome AF: 0.00692

Gnomad4 FIN exome AF: 0.00473

Gnomad4 NFE exome AF: 0.00503

Gnomad4 OTH exome AF: 0.00644

GnomAD4 genome AF: 0.0132 AC: 1835 AN: 138866 Hom.: 22 Cov.: 0 AF XY: 0.0122 AC XY: 811 AN XY: 66706

Gnomad4 AFR AF: 0.0351

Gnomad4 AMR AF: 0.00903

Gnomad4 ASJ AF: 0.0146

Gnomad4 EAS AF: 0.00167

Gnomad4 SAS AF: 0.00234

Gnomad4 FIN AF: 0.00285

Gnomad4 NFE AF: 0.00441

Gnomad4 OTH AF: 0.0101

ClinVar

Not reported in ClinVar

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: rs35953031; hg19: chr14-89087278;