Genetic Variant NM_006963.5:c.*730A>G (chr10-45004773-A-G) – 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.*730A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 166,938 control chromosomes in the GnomAD database, including 5,225 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 0.20 ( 5198 hom., cov: 32)

Exomes 𝑓: 0.061 ( 27 hom. )

Consequence

ZNF22
NM_006963.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.88

Publications

5 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF22	NM_006963.5 link	c.*730A>G		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.*730A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_006963.5	ENSP00000298299.3		P17026

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29649

AN:

151932

Hom.:

5177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.456

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.0523

Gnomad EAS

AF:

0.334

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.0624

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0586

Gnomad OTH

AF:

0.160

GnomAD4 exome

AF:

0.0611

AC:

909

AN:

14888

Hom.:

Cov.:

AF XY:

0.0601

AC XY:

425

AN XY:

7068

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0608

AC:

893

AN:

14698

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0698

AC:

AN:

Other (OTH)

AF:

0.100

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

102

153

204

255

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.195

AC:

29712

AN:

152050

Hom.:

5198

Cov.:

AF XY:

0.196

AC XY:

14543

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.456

AC:

18909

AN:

41440

American (AMR)

AF:

0.190

AC:

2899

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0523

AC:

181

AN:

3464

East Asian (EAS)

AF:

0.333

AC:

1723

AN:

5168

South Asian (SAS)

AF:

0.184

AC:

886

AN:

4810

European-Finnish (FIN)

AF:

0.0624

AC:

660

AN:

10572

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0586

AC:

3987

AN:

67992

Other (OTH)

AF:

0.160

AC:

337

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

998

1996

2994

3992

4990

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.116

Hom.:

3260

Bravo

AF:

0.219

Asia WGS

AF:

0.278

AC:

965

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

0.25

(source)

DANN

Benign

0.39

PhyloP100

-2.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over