Genetic Variant ZC3H14:c.*9196_*9200delAAAAA (chr14-88620934-TAAAAA-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_024824.5(ZC3H14):c.*9196_*9200delAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000255 in 1,372,336 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 0.0000072 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000028 ( 0 hom. )

Consequence

ZC3H14
NM_024824.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.833

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]

ZC3H14 links:

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

EML5 links:

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ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024824.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZC3H14	NM_024824.5	MANE Select	c.9196_9200delAAAAA	3_prime_UTR	Exon 17 of 17	NP_079100.2
EML5	NM_183387.3	MANE Select	c.5203-13_5203-9delTTTTT	intron	N/A	NP_899243.1	Q05BV3-5
ZC3H14	NM_001160103.2		c.9196_9200delAAAAA	3_prime_UTR	Exon 17 of 17	NP_001153575.1	Q6PJT7-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZC3H14	ENST00000251038.10	TSL:1 MANE Select	c.9196_9200delAAAAA	3_prime_UTR	Exon 17 of 17	ENSP00000251038.5	Q6PJT7-1
EML5	ENST00000554922.6	TSL:5 MANE Select	c.5203-13_5203-9delTTTTT	intron	N/A	ENSP00000451998.1	Q05BV3-5
EML5	ENST00000380664.9	TSL:5	c.5179-13_5179-9delTTTTT	intron	N/A	ENSP00000370039.5	Q05BV3-1

Frequencies

GnomAD3 genomes

AF:

0.00000720

AC:

AN:

138870

Hom.:

Cov.:

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:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000154

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000276

AC:

AN:

1233466

Hom.:

AF XY:

0.0000299

AC XY:

AN XY:

601150

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:

AN:

26824

American (AMR)

AF:

0.0000592

AC:

AN:

16892

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18588

East Asian (EAS)

AF:

0.00

AC:

AN:

33090

South Asian (SAS)

AF:

0.000207

AC:

AN:

58006

European-Finnish (FIN)

AF:

0.0000273

AC:

AN:

36628

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4892

European-Non Finnish (NFE)

AF:

0.0000182

AC:

AN:

987452

Other (OTH)

AF:

0.0000391

AC:

AN:

51094

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.250

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

AF:

0.00000720

AC:

AN:

138870

Hom.:

Cov.:

AF XY:

0.0000150

AC XY:

AN XY:

66682

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:

AN:

37352

American (AMR)

AF:

0.00

AC:

AN:

13820

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3366

East Asian (EAS)

AF:

0.00

AC:

AN:

4796

South Asian (SAS)

AF:

0.00

AC:

AN:

4296

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7380

Middle Eastern (MID)

AF:

0.00

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.0000154

AC:

AN:

64818

Other (OTH)

AF:

0.00

AC:

AN:

1870

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.275

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.83

Splicing

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

Publications

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14-88620934-TAAAAAA-TA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over