Genetic Variant ZNF22:c.*308T>C (chr10-45004351-T-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_006963.5(ZNF22):c.*308T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 247,318 control chromosomes in the GnomAD database, including 71,604 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 0.76 ( 44457 hom., cov: 32)

Exomes 𝑓: 0.75 ( 27147 hom. )

Consequence

ZNF22
NM_006963.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40

Publications

7 publications found

Variant links:

Genes affected

ZNF22 (HGNC:13012): (zinc finger protein 22) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF22 links:

ZNF22-AS1 (HGNC:23509): (ZNF22 antisense RNA 1) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ZNF22-AS1 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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF22	NM_006963.5 link	c.*308T>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000298299.4	NP_008894.2	P17026A0A024R7T4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF22	ENST00000298299.4 link	c.*308T>C		3_prime_UTR_variant	Exon 2 of 2	1	NM_006963.5	ENSP00000298299.3		P17026

Frequencies

GnomAD3 genomes

AF:

0.764

AC:

116128

AN:

152018

Hom.:

44420

Cov.:

show subpopulations

Gnomad AFR

AF:

0.781

Gnomad AMI

AF:

0.612

Gnomad AMR

AF:

0.789

Gnomad ASJ

AF:

0.673

Gnomad EAS

AF:

0.613

Gnomad SAS

AF:

0.750

Gnomad FIN

AF:

0.788

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.765

Gnomad OTH

AF:

0.751

GnomAD4 exome

AF:

0.753

AC:

71666

AN:

95182

Hom.:

27147

Cov.:

AF XY:

0.753

AC XY:

36220

AN XY:

48104

show subpopulations

African (AFR)

AF:

0.802

AC:

2240

AN:

2792

American (AMR)

AF:

0.790

AC:

3242

AN:

4104

Ashkenazi Jewish (ASJ)

AF:

0.684

AC:

2142

AN:

3132

East Asian (EAS)

AF:

0.571

AC:

3410

AN:

5968

South Asian (SAS)

AF:

0.746

AC:

1837

AN:

2462

European-Finnish (FIN)

AF:

0.785

AC:

14096

AN:

17952

Middle Eastern (MID)

AF:

0.675

AC:

251

AN:

372

European-Non Finnish (NFE)

AF:

0.761

AC:

40250

AN:

52858

Other (OTH)

AF:

0.757

AC:

4198

AN:

5542

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

857

1714

2571

3428

4285

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

246

492

738

984

1230

<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:

0.764

AC:

116222

AN:

152136

Hom.:

44457

Cov.:

AF XY:

0.766

AC XY:

56939

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.781

AC:

32403

AN:

41508

American (AMR)

AF:

0.789

AC:

12062

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.673

AC:

2333

AN:

3468

East Asian (EAS)

AF:

0.613

AC:

3168

AN:

5166

South Asian (SAS)

AF:

0.748

AC:

3611

AN:

4828

European-Finnish (FIN)

AF:

0.788

AC:

8324

AN:

10568

Middle Eastern (MID)

AF:

0.660

AC:

194

AN:

294

European-Non Finnish (NFE)

AF:

0.764

AC:

51976

AN:

67988

Other (OTH)

AF:

0.754

AC:

1595

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1431

2862

4293

5724

7155

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

866

1732

2598

3464

4330

<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:

0.759

Hom.:

148140

Bravo

AF:

0.765

Asia WGS

AF:

0.725

AC:

2519

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.5

(source)

DANN

Benign

0.65

PhyloP100

1.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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