Menu
GeneBe

7-112318211-A-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_021994.3(ZNF277):c.495A>G(p.Glu165=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00202 in 1,613,446 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 21 hom. )

Consequence

ZNF277
NM_021994.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.772
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-112318211-A-G is Benign according to our data. Variant chr7-112318211-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2657948.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.772 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF277NM_021994.3 linkuse as main transcriptc.495A>G p.Glu165= synonymous_variant 5/12 ENST00000361822.8
ZNF277XM_011515768.4 linkuse as main transcriptc.261A>G p.Glu87= synonymous_variant 5/12
ZNF277XM_017011720.3 linkuse as main transcriptc.141A>G p.Glu47= synonymous_variant 4/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF277ENST00000361822.8 linkuse as main transcriptc.495A>G p.Glu165= synonymous_variant 5/121 NM_021994.3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00166
AC:
252
AN:
152070
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000145
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000656
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0119
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00174
Gnomad OTH
AF:
0.000479
GnomAD3 exomes
AF:
0.00216
AC:
543
AN:
251192
Hom.:
4
AF XY:
0.00224
AC XY:
304
AN XY:
135764
show subpopulations
Gnomad AFR exome
AF:
0.000185
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0116
Gnomad NFE exome
AF:
0.00247
Gnomad OTH exome
AF:
0.00131
GnomAD4 exome
AF:
0.00206
AC:
3015
AN:
1461258
Hom.:
21
Cov.:
30
AF XY:
0.00201
AC XY:
1463
AN XY:
726926
show subpopulations
Gnomad4 AFR exome
AF:
0.000179
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00968
Gnomad4 NFE exome
AF:
0.00218
Gnomad4 OTH exome
AF:
0.00116
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00166
AC:
252
AN:
152188
Hom.:
3
Cov.:
32
AF XY:
0.00208
AC XY:
155
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.000144
Gnomad4 AMR
AF:
0.0000655
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0119
Gnomad4 NFE
AF:
0.00174
Gnomad4 OTH
AF:
0.000474
Alfa
AF:
0.00157
Hom.:
1
Bravo
AF:
0.000941
EpiCase
AF:
0.00180
EpiControl
AF:
0.00190

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenAug 01, 2023ZNF277: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.43
Cadd
Benign
5.8
Dann
Benign
0.62
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.

Other links and lift over

dbSNP: rs138489628; hg19: chr7-111958266; API