dbSNP rs3810291: ZC3H4:c.*610C>T (chr19-47065746-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015168.2(ZC3H4):c.*610C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 152,596 control chromosomes in the GnomAD database, including 22,476 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.50 ( 22360 hom., cov: 31)

Exomes 𝑓: 0.57 ( 116 hom. )

Consequence

ZC3H4
NM_015168.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.520

Publications

205 publications found

Variant links:

Genes affected

ZC3H4 (HGNC:17808): (zinc finger CCCH-type containing 4) This gene encodes a member of a family of CCCH (C-x8-C-x5-C-x3-H type) zinc finger domain-containing proteins. These zinc finger domains, which coordinate zinc finger binding and are characterized by three cysteine residues and one histidine residue, are nucleic acid-binding. Other family members are known to function in post-transcriptional regulation. [provided by RefSeq, Aug 2011]

ZC3H4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZC3H4	NM_015168.2 link	c.*610C>T		3_prime_UTR_variant	Exon 15 of 15	ENST00000253048.10	NP_055983.1	Q9UPT8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZC3H4	ENST00000253048.10 link	c.*610C>T	3_prime_UTR_variant	Exon 15 of 15	1	NM_015168.2	ENSP00000253048.4	Q9UPT8
ZC3H4	ENST00000594019.5 link	n.2372C>T	non_coding_transcript_exon_variant	Exon 7 of 7	2
ZC3H4	ENST00000601973.1 link	c.*610C>T	3_prime_UTR_variant	Exon 8 of 8	5		ENSP00000469684.1	M0QY97

Frequencies

GnomAD3 genomes

AF:

0.500

AC:

75872

AN:

151848

Hom.:

22358

Cov.:

show subpopulations

Gnomad AFR

AF:

0.189

Gnomad AMI

AF:

0.642

Gnomad AMR

AF:

0.530

Gnomad ASJ

AF:

0.648

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.623

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.675

Gnomad OTH

AF:

0.519

GnomAD4 exome

AF:

0.575

AC:

362

AN:

630

Hom.:

116

Cov.:

AF XY:

0.581

AC XY:

201

AN XY:

346

show subpopulations

African (AFR)

AF:

0.125

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.667

AC:

AN:

East Asian (EAS)

AF:

0.167

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.601

AC:

155

AN:

258

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.657

AC:

180

AN:

274

Other (OTH)

AF:

0.591

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.499

AC:

75875

AN:

151966

Hom.:

22360

Cov.:

AF XY:

0.496

AC XY:

36865

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.188

AC:

7806

AN:

41450

American (AMR)

AF:

0.530

AC:

8091

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.648

AC:

2248

AN:

3468

East Asian (EAS)

AF:

0.277

AC:

1431

AN:

5174

South Asian (SAS)

AF:

0.416

AC:

2007

AN:

4820

European-Finnish (FIN)

AF:

0.623

AC:

6577

AN:

10560

Middle Eastern (MID)

AF:

0.572

AC:

167

AN:

292

European-Non Finnish (NFE)

AF:

0.675

AC:

45875

AN:

67920

Other (OTH)

AF:

0.517

AC:

1089

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1584

3168

4753

6337

7921

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

648

1296

1944

2592

3240

<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:

0.627

Hom.:

111205

Bravo

AF:

0.481

Asia WGS

AF:

0.358

AC:

1246

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.60

(source)

DANN

Benign

0.43

PhyloP100

-0.52

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over