7-64706432-A-G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001282359.2(ZNF107):​c.335A>G​(p.Gln112Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,461,380 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.000010 ( 0 hom. )

Consequence

ZNF107
NM_001282359.2 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.734

Publications

0 publications found
Variant links:
Genes affected
ZNF107 (HGNC:12887): (zinc finger protein 107) This gene encodes a protein containing multiple C2H2-type zinc finger regions. Proteins containing zinc fingers may act as transcriptional regulators, but may also have other cellular functions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.13647693).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF107NM_001282359.2 linkc.335A>G p.Gln112Arg missense_variant Exon 4 of 4 ENST00000620827.6 NP_001269288.1 A0A0B4J2G0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF107ENST00000620827.6 linkc.335A>G p.Gln112Arg missense_variant Exon 4 of 4 4 NM_001282359.2 ENSP00000483720.1 A0A0B4J2G0

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.0000103
AC:
15
AN:
1461380
Hom.:
0
Cov.:
32
AF XY:
0.00000688
AC XY:
5
AN XY:
726916
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33464
American (AMR)
AF:
0.00
AC:
0
AN:
44698
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26118
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39668
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86168
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53390
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
0.0000126
AC:
14
AN:
1111740
Other (OTH)
AF:
0.0000166
AC:
1
AN:
60368
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.478
Heterozygous variant carriers
0
1
2
4
5
6
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.:
33
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jun 07, 2024
Ambry Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The c.128A>G (p.Q43R) alteration is located in exon 7 (coding exon 2) of the ZNF107 gene. This alteration results from a A to G substitution at nucleotide position 128, causing the glutamine (Q) at amino acid position 43 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.091
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.57
CADD
Benign
4.8
DANN
Benign
0.88
DEOGEN2
Benign
0.023
T;.;T;T;T;T
Eigen
Benign
-0.24
Eigen_PC
Benign
-0.56
FATHMM_MKL
Benign
0.00060
N
LIST_S2
Benign
0.24
T;T;T;.;T;.
M_CAP
Benign
0.0032
T
MetaRNN
Benign
0.14
T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.8
.;.;.;M;M;M
PhyloP100
0.73
PrimateAI
Benign
0.25
T
PROVEAN
Uncertain
-3.1
.;.;D;N;N;N
REVEL
Benign
0.057
Sift
Benign
0.035
.;.;D;T;T;T
Sift4G
Benign
0.37
T;T;D;T;T;T
Polyphen
0.97
.;.;.;D;D;D
Vest4
0.084
MutPred
0.55
.;.;Gain of MoRF binding (P = 0.0212);Gain of MoRF binding (P = 0.0212);Gain of MoRF binding (P = 0.0212);Gain of MoRF binding (P = 0.0212);
MVP
0.18
MPC
0.025
ClinPred
0.36
T
GERP RS
1.4
Varity_R
0.046
gMVP
0.026
Mutation Taster
=100/0
polymorphism

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: rs754017811; hg19: chr7-64166810; API