Variant chr11-6955757-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000278319.10(ZNF215):c.780A>T(p.Gly260=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 1,608,472 control chromosomes in the GnomAD database, including 438,913 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 0.68 ( 35528 hom., cov: 32)

Exomes 𝑓: 0.74 ( 403385 hom. )

Consequence

ZNF215
ENST00000278319.10 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.723

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 links:

LOC102724711 (HGNC:):

LOC102724711 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP7

Synonymous conserved (PhyloP=0.723 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF215	NM_013250.4 linkuse as main transcript	c.780A>T	p.Gly260=	synonymous_variant	7/7	ENST00000278319.10	NP_037382.2
LOC102724711	XR_002957236.2 linkuse as main transcript	n.1997T>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF215	ENST00000278319.10 linkuse as main transcript	c.780A>T	p.Gly260=	synonymous_variant	7/7	1	NM_013250.4	ENSP00000278319	P1	Q9UL58-1

Frequencies

GnomAD3 genomes

AF:

0.675

AC:

102573

AN:

151872

Hom.:

35516

Cov.:

show subpopulations

Gnomad AFR

AF:

0.494

Gnomad AMI

AF:

0.687

Gnomad AMR

AF:

0.749

Gnomad ASJ

AF:

0.698

Gnomad EAS

AF:

0.726

Gnomad SAS

AF:

0.802

Gnomad FIN

AF:

0.739

Gnomad MID

AF:

0.687

Gnomad NFE

AF:

0.744

Gnomad OTH

AF:

0.685

GnomAD3 exomes

AF:

0.739

AC:

181844

AN:

245972

Hom.:

67990

AF XY:

0.746

AC XY:

99037

AN XY:

132768

show subpopulations

Gnomad AFR exome

AF:

0.482

Gnomad AMR exome

AF:

0.814

Gnomad ASJ exome

AF:

0.700

Gnomad EAS exome

AF:

0.732

Gnomad SAS exome

AF:

0.810

Gnomad FIN exome

AF:

0.736

Gnomad NFE exome

AF:

0.741

Gnomad OTH exome

AF:

0.730

GnomAD4 exome

AF:

0.743

AC:

1081469

AN:

1456482

Hom.:

403385

Cov.:

AF XY:

0.746

AC XY:

539986

AN XY:

724242

show subpopulations

Gnomad4 AFR exome

AF:

0.488

Gnomad4 AMR exome

AF:

0.804

Gnomad4 ASJ exome

AF:

0.701

Gnomad4 EAS exome

AF:

0.738

Gnomad4 SAS exome

AF:

0.805

Gnomad4 FIN exome

AF:

0.735

Gnomad4 NFE exome

AF:

0.745

Gnomad4 OTH exome

AF:

0.726

GnomAD4 genome

AF:

0.675

AC:

102616

AN:

151990

Hom.:

35528

Cov.:

AF XY:

0.677

AC XY:

50252

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.494

Gnomad4 AMR

AF:

0.750

Gnomad4 ASJ

AF:

0.698

Gnomad4 EAS

AF:

0.726

Gnomad4 SAS

AF:

0.802

Gnomad4 FIN

AF:

0.739

Gnomad4 NFE

AF:

0.744

Gnomad4 OTH

AF:

0.688

Alfa

AF:

0.712

Hom.:

10379

Bravo

AF:

0.665

Asia WGS

AF:

0.758

AC:

2635

AN:

3478

EpiCase

AF:

0.735

EpiControl

AF:

0.737

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.5

DANN

Benign

0.46

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over