GeneBe

14-88620934-TAAAAAA-T

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_024824.5(ZC3H14):​c.*9195_*9200delAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000243 in 1,233,558 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: not found (cov: 0)
Exomes 𝑓: 0.0000024 ( 0 hom. )

Consequence

ZC3H14
NM_024824.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.83

Publications

0 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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZC3H14NM_024824.5 linkc.*9195_*9200delAAAAAA 3_prime_UTR_variant Exon 17 of 17 ENST00000251038.10 NP_079100.2 Q6PJT7-1
EML5NM_183387.3 linkc.5203-14_5203-9delTTTTTT 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.*9195_*9200delAAAAAA 3_prime_UTR_variant Exon 17 of 17 1 NM_024824.5 ENSP00000251038.5 Q6PJT7-1
EML5ENST00000554922.6 linkc.5203-14_5203-9delTTTTTT intron_variant Intron 38 of 43 5 NM_183387.3 ENSP00000451998.1 Q05BV3-5

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000243
AC:
3
AN:
1233558
Hom.:
0
AF XY:
0.00000333
AC XY:
2
AN XY:
601192
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
26826
American (AMR)
AF:
0.00
AC:
0
AN:
16898
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
18590
East Asian (EAS)
AF:
0.0000302
AC:
1
AN:
33090
South Asian (SAS)
AF:
0.00
AC:
0
AN:
58012
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
36638
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4892
European-Non Finnish (NFE)
AF:
0.00000203
AC:
2
AN:
987514
Other (OTH)
AF:
0.00
AC:
0
AN:
51098
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000047), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.308
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.8

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