9-111530912-G-A

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_133464.5(ZNF483):​c.450G>A​(p.Glu150Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000969 in 1,548,304 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000073 ( 0 hom., cov: 26)
Exomes 𝑓: 0.000099 ( 0 hom. )

Consequence

ZNF483
NM_133464.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.751

Publications

0 publications found
Variant links:
Genes affected
ZNF483 (HGNC:23384): (zinc finger protein 483) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 9-111530912-G-A is Benign according to our data. Variant chr9-111530912-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3987490.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.751 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF483NM_133464.5 linkc.450G>A p.Glu150Glu synonymous_variant Exon 3 of 6 ENST00000309235.6 NP_597721.2 Q8TF39-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF483ENST00000309235.6 linkc.450G>A p.Glu150Glu synonymous_variant Exon 3 of 6 1 NM_133464.5 ENSP00000311679.5 Q8TF39-1
ZNF483ENST00000355824.7 linkc.450G>A p.Glu150Glu synonymous_variant Exon 3 of 6 1 ENSP00000438048.1 Q6P088
ZNF483ENST00000358151.8 linkc.450G>A p.Glu150Glu synonymous_variant Exon 3 of 6 2 ENSP00000350871.4 Q8TF39-2

Frequencies

GnomAD3 genomes
AF:
0.0000732
AC:
11
AN:
150212
Hom.:
0
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000199
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000889
Gnomad OTH
AF:
0.000972
GnomAD2 exomes
AF:
0.0000695
AC:
17
AN:
244718
AF XY:
0.0000680
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000244
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000463
Gnomad NFE exome
AF:
0.0000718
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000994
AC:
139
AN:
1397982
Hom.:
0
Cov.:
28
AF XY:
0.000105
AC XY:
73
AN XY:
695934
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
32376
American (AMR)
AF:
0.000233
AC:
10
AN:
42960
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
23928
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37698
South Asian (SAS)
AF:
0.00
AC:
0
AN:
80484
European-Finnish (FIN)
AF:
0.0000206
AC:
1
AN:
48442
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5492
European-Non Finnish (NFE)
AF:
0.000116
AC:
124
AN:
1070112
Other (OTH)
AF:
0.0000708
AC:
4
AN:
56490
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.439
Heterozygous variant carriers
0
5
10
15
20
25
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
10
20
30
40
50
<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
AF:
0.0000732
AC:
11
AN:
150322
Hom.:
0
Cov.:
26
AF XY:
0.0000818
AC XY:
6
AN XY:
73386
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
41046
American (AMR)
AF:
0.000199
AC:
3
AN:
15068
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3446
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5118
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4720
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10196
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
286
European-Non Finnish (NFE)
AF:
0.0000889
AC:
6
AN:
67458
Other (OTH)
AF:
0.000962
AC:
2
AN:
2080
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.448
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome 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
Alfa
AF:
0.0000987
Hom.:
0
Bravo
AF:
0.0000680

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Jun 07, 2025
Ambry Genetics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
5.4
DANN
Benign
0.54
PhyloP100
0.75

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs200679867; hg19: chr9-114293192; API