Genetic Variant ZC3H14:c.*9197_*9200delAAAA (chr14-88620934-TAAAA-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.*9197_*9200delAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 1,371,254 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 0.000014 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00022 ( 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.9197_9200delAAAA	3_prime_UTR	Exon 17 of 17	NP_079100.2
EML5	NM_183387.3	MANE Select	c.5203-12_5203-9delTTTT	intron	N/A	NP_899243.1	Q05BV3-5
ZC3H14	NM_001160103.2		c.9197_9200delAAAA	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.9197_9200delAAAA	3_prime_UTR	Exon 17 of 17	ENSP00000251038.5	Q6PJT7-1
EML5	ENST00000554922.6	TSL:5 MANE Select	c.5203-12_5203-9delTTTT	intron	N/A	ENSP00000451998.1	Q05BV3-5
EML5	ENST00000380664.9	TSL:5	c.5179-12_5179-9delTTTT	intron	N/A	ENSP00000370039.5	Q05BV3-1

Frequencies

GnomAD3 genomes

AF:

0.0000144

AC:

AN:

138868

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:

0.0000309

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00193

AC:

101

AN:

52316

AF XY:

0.00220

show subpopulations

Gnomad AFR exome

AF:

0.000937

Gnomad AMR exome

AF:

0.00176

Gnomad ASJ exome

AF:

0.00396

Gnomad EAS exome

AF:

0.00176

Gnomad FIN exome

AF:

0.000474

Gnomad NFE exome

AF:

0.00179

Gnomad OTH exome

AF:

0.00220

GnomAD4 exome

AF:

0.000216

AC:

266

AN:

1232386

Hom.:

AF XY:

0.000253

AC XY:

152

AN XY:

600626

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000299

AC:

AN:

26796

American (AMR)

AF:

0.00119

AC:

AN:

16856

Ashkenazi Jewish (ASJ)

AF:

0.000539

AC:

AN:

18568

East Asian (EAS)

AF:

0.000212

AC:

AN:

33054

South Asian (SAS)

AF:

0.000846

AC:

AN:

57888

European-Finnish (FIN)

AF:

0.000246

AC:

AN:

36588

Middle Eastern (MID)

AF:

0.000409

AC:

AN:

4890

European-Non Finnish (NFE)

AF:

0.000149

AC:

147

AN:

986710

Other (OTH)

AF:

0.000274

AC:

AN:

51036

⚠️ 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: 0.258

Heterozygous variant carriers

130

162

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:

0.0000144

AC:

AN:

138868

Hom.:

Cov.:

AF XY:

0.0000300

AC XY:

AN XY:

66684

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

37352

American (AMR)

AF:

0.00

AC:

AN:

13816

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:

0.0000309

AC:

AN:

64820

Other (OTH)

AF:

0.00

AC:

AN:

1870

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.375

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.83

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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

Publications

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14-88620934-TAAAAAA-TAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over