Genetic Variant ZC3H14:c.235+14_235+15insAT (chr14-88571138-C-CAT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_024824.5(ZC3H14):c.235+14_235+15insAT variant causes a intron 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 0.61 ( 29929 hom., cov: 0)

Exomes 𝑓: 0.63 ( 235987 hom. )

Consequence

ZC3H14
NM_024824.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.33

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 Gene-Disease associations (from GenCC):

autosomal recessive non-syndromic intellectual disability
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
intellectual disability
Inheritance: AR Classification: LIMITED Submitted by: ClinGen
intellectual disability, autosomal recessive 56
Inheritance: AR, AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ZC3H14 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

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.235+14_235+15insAT	intron	N/A	NP_079100.2
ZC3H14	NM_001160103.2		c.235+14_235+15insAT	intron	N/A	NP_001153575.1	Q6PJT7-2
ZC3H14	NM_001326310.2		c.235+14_235+15insAT	intron	N/A	NP_001313239.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZC3H14	ENST00000251038.10	TSL:1 MANE Select	c.235+14_235+15insAT	intron	N/A	ENSP00000251038.5	Q6PJT7-1
ZC3H14	ENST00000302216.12	TSL:1	c.235+14_235+15insAT	intron	N/A	ENSP00000307025.8	Q6PJT7-3
ZC3H14	ENST00000336693.8	TSL:1	c.133+14_133+15insAT	intron	N/A	ENSP00000338002.4	Q6PJT7-4

Frequencies

GnomAD3 genomes

AF:

0.614

AC:

92450

AN:

150630

Hom.:

29915

Cov.:

show subpopulations

Gnomad AFR

AF:

0.418

Gnomad AMI

AF:

0.611

Gnomad AMR

AF:

0.545

Gnomad ASJ

AF:

0.667

Gnomad EAS

AF:

0.399

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.786

Gnomad MID

AF:

0.624

Gnomad NFE

AF:

0.735

Gnomad OTH

AF:

0.635

GnomAD2 exomes

AF:

0.581

AC:

112470

AN:

193698

AF XY:

0.587

show subpopulations

Gnomad AFR exome

AF:

0.409

Gnomad AMR exome

AF:

0.411

Gnomad ASJ exome

AF:

0.586

Gnomad EAS exome

AF:

0.376

Gnomad FIN exome

AF:

0.747

Gnomad NFE exome

AF:

0.672

Gnomad OTH exome

AF:

0.604

GnomAD4 exome

AF:

0.627

AC:

814885

AN:

1299342

Hom.:

235987

Cov.:

AF XY:

0.625

AC XY:

404384

AN XY:

646830

show subpopulations

African (AFR)

AF:

0.371

AC:

11294

AN:

30444

American (AMR)

AF:

0.402

AC:

15847

AN:

39420

Ashkenazi Jewish (ASJ)

AF:

0.595

AC:

13815

AN:

23208

East Asian (EAS)

AF:

0.351

AC:

12824

AN:

36576

South Asian (SAS)

AF:

0.502

AC:

36976

AN:

73720

European-Finnish (FIN)

AF:

0.709

AC:

34100

AN:

48118

Middle Eastern (MID)

AF:

0.559

AC:

2924

AN:

5228

European-Non Finnish (NFE)

AF:

0.662

AC:

655095

AN:

988962

Other (OTH)

AF:

0.596

AC:

32010

AN:

53666

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

11707

23414

35121

46828

58535

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17774

35548

53322

71096

88870

<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:

0.614

AC:

92493

AN:

150734

Hom.:

29929

Cov.:

AF XY:

0.613

AC XY:

45117

AN XY:

73610

show subpopulations

African (AFR)

AF:

0.418

AC:

17117

AN:

40978

American (AMR)

AF:

0.545

AC:

8256

AN:

15144

Ashkenazi Jewish (ASJ)

AF:

0.667

AC:

2304

AN:

3452

East Asian (EAS)

AF:

0.400

AC:

2051

AN:

5128

South Asian (SAS)

AF:

0.597

AC:

2854

AN:

4780

European-Finnish (FIN)

AF:

0.786

AC:

8086

AN:

10288

Middle Eastern (MID)

AF:

0.620

AC:

181

AN:

292

European-Non Finnish (NFE)

AF:

0.735

AC:

49760

AN:

67670

Other (OTH)

AF:

0.635

AC:

1332

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1615

3230

4846

6461

8076

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

760

1520

2280

3040

3800

<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:

0.562

Hom.:

2617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-2.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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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