dbSNP rs2766671: ZNF217:c.*1325G>A (chr20-53567963-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_006526.3(ZNF217):c.*1325G>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 0.0861 in 152,556 control chromosomes in the GnomAD database, including 748 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 0.086 ( 743 hom., cov: 32)

Exomes 𝑓: 0.14 ( 5 hom. )

Consequence

ZNF217
NM_006526.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.847

Publications

4 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:

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=-0.85).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF217	NM_006526.3 link	c.*1325G>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000371471.7	NP_006517.1	O75362

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZNF217	ENST00000371471.7 link	c.*1325G>A	3_prime_UTR_variant	Exon 6 of 6	5	NM_006526.3	ENSP00000360526.2	O75362
ZNF217	ENST00000302342.3 link	c.*1325G>A	3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000304308.3	O75362
ZNF217-AS1	ENST00000424252.2 link	n.556-2309C>T	intron_variant	Intron 3 of 5	2

Frequencies

GnomAD3 genomes

AF:

0.0860

AC:

13080

AN:

152016

Hom.:

743

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0226

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0820

Gnomad ASJ

AF:

0.0588

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.0400

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.0843

GnomAD4 exome

AF:

0.140

AC:

AN:

422

Hom.:

Cov.:

AF XY:

0.154

AC XY:

AN XY:

254

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:

0.139

AC:

AN:

416

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: 0.494

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0860

AC:

13079

AN:

152134

Hom.:

743

Cov.:

AF XY:

0.0843

AC XY:

6271

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.0225

AC:

936

AN:

41520

American (AMR)

AF:

0.0818

AC:

1248

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.0588

AC:

204

AN:

3470

East Asian (EAS)

AF:

0.000964

AC:

AN:

5186

South Asian (SAS)

AF:

0.0400

AC:

193

AN:

4826

European-Finnish (FIN)

AF:

0.141

AC:

1488

AN:

10572

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.128

AC:

8701

AN:

67986

Other (OTH)

AF:

0.0834

AC:

176

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

610

1220

1831

2441

3051

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:

0.111

Hom.:

1676

Bravo

AF:

0.0787

Asia WGS

AF:

0.0190

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.2

(source)

DANN

Benign

0.54

PhyloP100

0.85

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