GeneBe

16-89721839-G-T

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001113525.2(ZNF276):​c.199G>T​(p.Glu67*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000189 in 1,060,392 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000019 ( 0 hom. )

Consequence

ZNF276
NM_001113525.2 stop_gained

Scores

2
2
3

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Publications

0 publications found
Variant links:
Genes affected
ZNF276 (HGNC:23330): (zinc finger protein 276) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in kinetochore. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF276NM_001113525.2 linkc.199G>T p.Glu67* stop_gained Exon 1 of 11 ENST00000443381.7 NP_001106997.1 Q8N554-1I6L9I3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF276ENST00000443381.7 linkc.199G>T p.Glu67* stop_gained Exon 1 of 11 1 NM_001113525.2 ENSP00000415836.2 Q8N554-1

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
0.00000189
AC:
2
AN:
1060392
Hom.:
0
Cov.:
31
AF XY:
0.00000200
AC XY:
1
AN XY:
500784
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
22020
American (AMR)
AF:
0.00
AC:
0
AN:
7674
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
13240
East Asian (EAS)
AF:
0.00
AC:
0
AN:
24468
South Asian (SAS)
AF:
0.00
AC:
0
AN:
19614
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
20778
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2790
European-Non Finnish (NFE)
AF:
0.00000110
AC:
1
AN:
907760
Other (OTH)
AF:
0.0000238
AC:
1
AN:
42048
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.61
D
BayesDel_noAF
Pathogenic
0.63
CADD
Pathogenic
38
DANN
Uncertain
0.99
Eigen
Uncertain
0.45
Eigen_PC
Benign
0.14
FATHMM_MKL
Benign
0.15
N
PhyloP100
1.3
Vest4
0.061
GERP RS
3.3
PromoterAI
-0.0083
Neutral
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

Other links and lift over

dbSNP: rs1486433152; hg19: chr16-89788247; API