Genetic Variant ZNF217:c.*2122G>A (chr20-53567166-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001385034.1(ZNF217):c.*1950G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0869 in 152,232 control chromosomes in the GnomAD database, including 741 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 0.087 ( 735 hom., cov: 33)

Exomes 𝑓: 0.15 ( 6 hom. )

Consequence

ZNF217
NM_001385034.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.790

Publications

6 publications found

Variant links:

Genes affected

ZNF217 (HGNC:13009): (zinc finger protein 217) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in mitochondrion and nuclear speck. Part of histone deacetylase complex. [provided by Alliance of Genome Resources, Apr 2022]

ZNF217 links:

ZNF217-AS1 (HGNC:56842): (ZNF217 antisense RNA 1)

ZNF217-AS1 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=-0.5).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385034.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF217	NM_006526.3	MANE Select	c.*2122G>A	3_prime_UTR	Exon 6 of 6	NP_006517.1
ZNF217	NM_001385034.1		c.*1950G>A	3_prime_UTR	Exon 5 of 5	NP_001371963.1
ZNF217-AS1	NR_110051.1		n.556-3106C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF217	ENST00000371471.7	TSL:5 MANE Select	c.*2122G>A	3_prime_UTR	Exon 6 of 6	ENSP00000360526.2
ZNF217	ENST00000302342.3	TSL:1	c.*2122G>A	3_prime_UTR	Exon 5 of 5	ENSP00000304308.3
ZNF217-AS1	ENST00000424252.2	TSL:2	n.556-3106C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0868

AC:

13163

AN:

151710

Hom.:

734

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0249

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0822

Gnomad ASJ

AF:

0.0589

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0403

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.0853

GnomAD4 exome

AF:

0.149

AC:

AN:

404

Hom.:

Cov.:

AF XY:

0.164

AC XY:

AN XY:

250

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)

AF:

0.148

AC:

AN:

398

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0868

AC:

13173

AN:

151828

Hom.:

735

Cov.:

AF XY:

0.0850

AC XY:

6307

AN XY:

74198

show subpopulations

African (AFR)

AF:

0.0249

AC:

1030

AN:

41442

American (AMR)

AF:

0.0821

AC:

1251

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.0589

AC:

204

AN:

3464

East Asian (EAS)

AF:

0.00116

AC:

AN:

5174

South Asian (SAS)

AF:

0.0403

AC:

194

AN:

4810

European-Finnish (FIN)

AF:

0.141

AC:

1472

AN:

10456

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.128

AC:

8700

AN:

67924

Other (OTH)

AF:

0.0892

AC:

188

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

618

1237

1855

2474

3092

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

280

420

560

700

<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:

0.112

Hom.:

338

Bravo

AF:

0.0795

Asia WGS

AF:

0.0300

AC:

103

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

0.79

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over