GeneBe

NM_024824.5:c.*9193_*9200dupAAAAAAAA

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_024824.5(ZC3H14):​c.*9193_*9200dupAAAAAAAA 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 0.0000072 ( 0 hom., cov: 0)

Consequence

ZC3H14
NM_024824.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.252

Publications

1 publications found
Variant links:
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]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZC3H14NM_024824.5 linkc.*9193_*9200dupAAAAAAAA 3_prime_UTR_variant Exon 17 of 17 ENST00000251038.10 NP_079100.2 Q6PJT7-1
EML5NM_183387.3 linkc.5203-16_5203-9dupTTTTTTTT intron_variant Intron 38 of 43 ENST00000554922.6 NP_899243.1 Q05BV3-5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZC3H14ENST00000251038.10 linkc.*9193_*9200dupAAAAAAAA 3_prime_UTR_variant Exon 17 of 17 1 NM_024824.5 ENSP00000251038.5 Q6PJT7-1
EML5ENST00000554922.6 linkc.5203-16_5203-9dupTTTTTTTT intron_variant Intron 38 of 43 5 NM_183387.3 ENSP00000451998.1 Q05BV3-5

Frequencies

GnomAD3 genomes
AF:
0.00000720
AC:
1
AN:
138874
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
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:
0.000135
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
0
GnomAD4 genome
AF:
0.00000720
AC:
1
AN:
138874
Hom.:
0
Cov.:
0
AF XY:
0.0000150
AC XY:
1
AN XY:
66686
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
37352
American (AMR)
AF:
0.00
AC:
0
AN:
13820
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3366
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4796
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4296
European-Finnish (FIN)
AF:
0.000135
AC:
1
AN:
7382
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
284
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
64820
Other (OTH)
AF:
0.00
AC:
0
AN:
1870
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs35953031; hg19: chr14-89087278; API