Genetic Variant ZNF334:c.-260T>G (chr20-46512761-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001353824.2(ZNF334):c.-260T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,056 control chromosomes in the GnomAD database, including 22,457 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 0.54 ( 22455 hom., cov: 32)

Exomes 𝑓: 0.75 ( 2 hom. )

Consequence

ZNF334
NM_001353824.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.70

Publications

11 publications found

Variant links:

Genes affected

ZNF334 (HGNC:15806): (zinc finger protein 334) This gene encodes a member of the C2H2 zinc finger family. The encoded protein contains a Krueppel-associated box, fourteen C2H2 zinc finger domains, and four C2H2-type/integrase DNA-binding domains. Decreased expression of this gene may be a marker for rheumatoid arthritis. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]

ZNF334 links:

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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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF334	NM_001353824.2 link	c.-260T>G		5_prime_UTR_variant	Exon 1 of 5	ENST00000692313.1	NP_001340753.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZNF334	ENST00000692313.1 link	c.-260T>G	5_prime_UTR_variant	Exon 1 of 5		NM_001353824.2	ENSP00000510334.1	Q9HCZ1
ZNF334	ENST00000347606.8 link	c.-38-621T>G	intron_variant	Intron 1 of 4	1		ENSP00000255129.5	Q9HCZ1
ZNF334	ENST00000457685.6 link	c.-526T>G	5_prime_UTR_variant	Exon 1 of 6	2		ENSP00000402582.1	A0A0B4J1Y0
ZNF334	ENST00000625284.2 link	c.-188-621T>G	intron_variant	Intron 1 of 5	2		ENSP00000485779.1	A0A087X1P4

Frequencies

GnomAD3 genomes

AF:

0.539

AC:

81861

AN:

151930

Hom.:

22399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.637

Gnomad AMI

AF:

0.638

Gnomad AMR

AF:

0.498

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.361

Gnomad SAS

AF:

0.559

Gnomad FIN

AF:

0.486

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.509

Gnomad OTH

AF:

0.531

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.539

AC:

81973

AN:

152048

Hom.:

22455

Cov.:

AF XY:

0.538

AC XY:

40022

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.638

AC:

26462

AN:

41470

American (AMR)

AF:

0.497

AC:

7603

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.517

AC:

1792

AN:

3468

East Asian (EAS)

AF:

0.361

AC:

1871

AN:

5180

South Asian (SAS)

AF:

0.559

AC:

2693

AN:

4816

European-Finnish (FIN)

AF:

0.486

AC:

5138

AN:

10564

Middle Eastern (MID)

AF:

0.490

AC:

144

AN:

294

European-Non Finnish (NFE)

AF:

0.509

AC:

34564

AN:

67950

Other (OTH)

AF:

0.533

AC:

1125

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1931

3863

5794

7726

9657

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

718

1436

2154

2872

3590

<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:

0.507

Hom.:

54348

Bravo

AF:

0.543

Asia WGS

AF:

0.513

AC:

1786

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.51

(source)

DANN

Benign

0.58

PhyloP100

-2.7

Mutation Taster

=299/1

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over