Variant chr7-112206716-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_021994.3(ZNF277):c.-1A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00747 in 1,613,132 control chromosomes in the GnomAD database, including 51 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0056 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0077 ( 47 hom. )

Consequence

ZNF277
NM_021994.3 5_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.182

Variant links:

Genes affected

ZNF277 (HGNC:13070): (zinc finger protein 277) Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and metal ion binding activity. Predicted to act upstream of or within cellular response to hydrogen peroxide and regulation of cellular senescence. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF277 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 7-112206716-A-G is Benign according to our data. Variant chr7-112206716-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2657946.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
ZNF277	NM_021994.3 linkuse as main transcript	c.-1A>G	5_prime_UTR_variant	1/12	ENST00000361822.8
ZNF277	XM_011515768.4 linkuse as main transcript	c.-231A>G	5_prime_UTR_variant	1/12
ZNF277	XM_017011720.3 linkuse as main transcript	c.-262A>G	5_prime_UTR_variant	1/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF277	ENST00000361822.8 linkuse as main transcript	c.-1A>G		5_prime_UTR_variant	1/12	1	NM_021994.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00556

AC:

846

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00171

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00648

Gnomad ASJ

AF:

0.0181

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00641

Gnomad FIN

AF:

0.00471

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00754

Gnomad OTH

AF:

0.00813

GnomAD3 exomes

AF:

0.00635

AC:

1576

AN:

248068

Hom.:

AF XY:

0.00688

AC XY:

927

AN XY:

134706

show subpopulations

Gnomad AFR exome

AF:

0.00165

Gnomad AMR exome

AF:

0.00454

Gnomad ASJ exome

AF:

0.0138

Gnomad EAS exome

AF:

0.0000549

Gnomad SAS exome

AF:

0.00729

Gnomad FIN exome

AF:

0.00366

Gnomad NFE exome

AF:

0.00815

Gnomad OTH exome

AF:

0.00682

GnomAD4 exome

AF:

0.00767

AC:

11198

AN:

1460792

Hom.:

Cov.:

AF XY:

0.00782

AC XY:

5681

AN XY:

726718

show subpopulations

Gnomad4 AFR exome

AF:

0.00159

Gnomad4 AMR exome

AF:

0.00542

Gnomad4 ASJ exome

AF:

0.0140

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00733

Gnomad4 FIN exome

AF:

0.00425

Gnomad4 NFE exome

AF:

0.00828

Gnomad4 OTH exome

AF:

0.00751

GnomAD4 genome

AF:

0.00555

AC:

846

AN:

152340

Hom.:

Cov.:

AF XY:

0.00502

AC XY:

374

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.00171

Gnomad4 AMR

AF:

0.00647

Gnomad4 ASJ

AF:

0.0181

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00600

Gnomad4 FIN

AF:

0.00471

Gnomad4 NFE

AF:

0.00757

Gnomad4 OTH

AF:

0.00804

Alfa

AF:

0.00514

Hom.:

Bravo

AF:

0.00576

EpiCase

AF:

0.00812

EpiControl

AF:

0.00849

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2023

ZNF277: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.77

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over