dbSNP rs11471: 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006963.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF22	NM_006963.5	MANE Select	c.*308T>C		3_prime_UTR	Exon 2 of 2	NP_008894.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF22	ENST00000298299.4	TSL:1 MANE Select	c.*308T>C	3_prime_UTR	Exon 2 of 2	ENSP00000298299.3	P17026
ZNF22-AS1	ENST00000456938.7	TSL:1	n.684-276A>G	intron	N/A
ZNF22	ENST00000870780.1		c.*308T>C	3_prime_UTR	Exon 2 of 2	ENSP00000540839.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over