dbSNP rs2638094: ZNF215:c.805+4475A>G (chr11-6960257-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 ENST00000529903.1(ZNF215):c.805+4475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,154 control chromosomes in the GnomAD database, including 2,163 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 0.16 ( 2163 hom., cov: 32)

Consequence

ZNF215
ENST00000529903.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540

Publications

5 publications found

Variant links:

Genes affected

ZNF215 (HGNC:13007): (zinc finger protein 215) This gene is imprinted in a tissue-specific manner with preferential expression in the testis, and encodes a zinc finger protein that belongs to a family of zinc finger transcription factors. The encoded protein contains an N-terminal SRE-ZBP, Ctfin51, AW-1, and Number 18 (SCAN) domain, a kruppel-associated box A (KRABA) domain, and four C-terminal zinc finger domains. This gene is located within one of three regions on chromosome 11p15 associated with Beckwith-Wiedemann syndrome, called Beckwith-Wiedemann syndrome chromosome region-2 (BWSCR2), and is thought to play a role in the etiology of this disease. [provided by RefSeq, Aug 2017]

ZNF215 Gene-Disease associations (from GenCC):

Beckwith-Wiedemann syndrome
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ZNF215 links:

LOC102724711 (HGNC:):

LOC102724711 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
ZNF215	NM_001354854.1 link	c.805+4475A>G	intron_variant	Intron 6 of 6	NP_001341783.1
ZNF215	NR_149005.2 link	n.1433+4475A>G	intron_variant	Intron 6 of 6
ZNF215	XM_024448683.2 link	c.805+4475A>G	intron_variant	Intron 7 of 7	XP_024304451.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ZNF215	ENST00000529903.1 link	c.805+4475A>G	intron_variant	Intron 5 of 5	1	ENSP00000432306.1	Q9UL58-2
ZNF215	ENST00000610573.4 link	c.805+4475A>G	intron_variant	Intron 7 of 7	5	ENSP00000484674.1	Q9UL58-2
ZNF215	ENST00000636097.1 link	n.*126+4475A>G	intron_variant	Intron 6 of 6	5	ENSP00000490414.1	B4DYW9
ZNF215	ENST00000636606.1 link	n.*87+4475A>G	intron_variant	Intron 5 of 6	5	ENSP00000490359.1	A0A1B0GV37

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23820

AN:

152036

Hom.:

2164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.0499

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.204

Gnomad OTH

AF:

0.165

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.157

AC:

23822

AN:

152154

Hom.:

2163

Cov.:

AF XY:

0.153

AC XY:

11368

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.102

AC:

4226

AN:

41510

American (AMR)

AF:

0.150

AC:

2295

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.232

AC:

805

AN:

3470

East Asian (EAS)

AF:

0.00231

AC:

AN:

5188

South Asian (SAS)

AF:

0.0508

AC:

245

AN:

4826

European-Finnish (FIN)

AF:

0.163

AC:

1727

AN:

10592

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.204

AC:

13900

AN:

67982

Other (OTH)

AF:

0.163

AC:

345

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1005

2010

3016

4021

5026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.184

Hom.:

1404

Bravo

AF:

0.154

Asia WGS

AF:

0.0350

AC:

124

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

5.4

(source)

DANN

Benign

0.67

PhyloP100

-0.054

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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