dbSNP rs2595500: ZNF215:c.483+281A>G (chr11-6941934-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_013250.4(ZNF215):c.483+281A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,226 control chromosomes in the GnomAD database, including 2,254 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 ( 2254 hom., cov: 32)

Consequence

ZNF215
NM_013250.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.30

Publications

8 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:

LOC107984019 (HGNC:):

LOC107984019 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013250.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF215	NM_013250.4	MANE Select	c.483+281A>G	intron	N/A	NP_037382.2	Q9UL58-1
ZNF215	NM_001354853.2		c.483+281A>G	intron	N/A	NP_001341782.1	Q9UL58-1
ZNF215	NM_001354854.1		c.483+281A>G	intron	N/A	NP_001341783.1	Q9UL58-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF215	ENST00000278319.10	TSL:1 MANE Select	c.483+281A>G	intron	N/A	ENSP00000278319.5	Q9UL58-1
ZNF215	ENST00000529903.1	TSL:1	c.483+281A>G	intron	N/A	ENSP00000432306.1	Q9UL58-2
ZNF215	ENST00000921289.1		c.483+281A>G	intron	N/A	ENSP00000591348.1

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24426

AN:

152108

Hom.:

2256

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.216

Gnomad EAS

AF:

0.00269

Gnomad SAS

AF:

0.0516

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.168

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

GnomAD4 genome

AF:

0.160

AC:

24429

AN:

152226

Hom.:

2254

Cov.:

AF XY:

0.156

AC XY:

11625

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.106

AC:

4415

AN:

41558

American (AMR)

AF:

0.158

AC:

2421

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.216

AC:

749

AN:

3470

East Asian (EAS)

AF:

0.00270

AC:

AN:

5190

South Asian (SAS)

AF:

0.0521

AC:

251

AN:

4818

European-Finnish (FIN)

AF:

0.164

AC:

1735

AN:

10600

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.209

AC:

14216

AN:

67982

Other (OTH)

AF:

0.166

AC:

350

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1039

2079

3118

4158

5197

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.179

Hom.:

1895

Bravo

AF:

0.159

Asia WGS

AF:

0.0400

AC:

143

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

1.3

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