rs769120990

Variant summary

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

The NM_001282359.2(ZNF107):​c.793G>A​(p.Ala265Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A265S) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000041 ( 0 hom. )

Consequence

ZNF107
NM_001282359.2 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.671

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=0.08159047).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF107NM_001282359.2 linkc.793G>A p.Ala265Thr 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.793G>A p.Ala265Thr missense_variant Exon 4 of 4 4 NM_001282359.2 ENSP00000483720.1 A0A0B4J2G0

Frequencies

GnomAD3 genomes
AF:
0.0000132
AC:
2
AN:
152062
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.0000121
AC:
3
AN:
248092
AF XY:
0.0000223
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000163
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000411
AC:
6
AN:
1461012
Hom.:
0
Cov.:
33
AF XY:
0.00000413
AC XY:
3
AN XY:
726820
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33424
American (AMR)
AF:
0.00
AC:
0
AN:
44636
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26028
East Asian (EAS)
AF:
0.000151
AC:
6
AN:
39676
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86148
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53302
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5758
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1111704
Other (OTH)
AF:
0.00
AC:
0
AN:
60336
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
1
1
2
2
3
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
AF:
0.0000132
AC:
2
AN:
152062
Hom.:
0
Cov.:
33
AF XY:
0.0000135
AC XY:
1
AN XY:
74248
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
41416
American (AMR)
AF:
0.00
AC:
0
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3472
East Asian (EAS)
AF:
0.000385
AC:
2
AN:
5190
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4828
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10604
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67976
Other (OTH)
AF:
0.00
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
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

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:
0.0000434
Hom.:
0
Bravo
AF:
0.00000756
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.49
T
BayesDel_noAF
Benign
-0.68
CADD
Benign
10
DANN
Benign
0.80
DEOGEN2
Benign
0.028
T;.;T;T;T
Eigen
Benign
-0.69
Eigen_PC
Benign
-0.82
FATHMM_MKL
Benign
0.000090
N
LIST_S2
Benign
0.068
T;T;.;T;.
M_CAP
Benign
0.0033
T
MetaRNN
Benign
0.082
T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.94
.;.;L;L;L
PhyloP100
-0.67
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-2.0
.;.;N;N;N
REVEL
Benign
0.043
Sift
Benign
0.24
.;.;T;T;T
Sift4G
Benign
0.24
T;T;T;T;T
Polyphen
0.93
.;.;P;P;P
Vest4
0.055
MutPred
0.37
.;.;Gain of loop (P = 0.1081);Gain of loop (P = 0.1081);Gain of loop (P = 0.1081);
MVP
0.061
MPC
0.0086
ClinPred
0.086
T
GERP RS
1.4
Varity_R
0.070
gMVP
0.0090
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: rs769120990; hg19: chr7-64167268; API