19-34957994-G-A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_175872.5(ZNF792):​c.1861C>T​(p.Leu621Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,306 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. L621I) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

ZNF792
NM_175872.5 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0150

Publications

0 publications found
Variant links:
Genes affected
ZNF792 (HGNC:24751): (zinc finger protein 792) Enables identical protein 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: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.041920274).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF792NM_175872.5 linkc.1861C>T p.Leu621Phe missense_variant Exon 4 of 4 ENST00000404801.2 NP_787068.3 Q3KQV3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF792ENST00000404801.2 linkc.1861C>T p.Leu621Phe missense_variant Exon 4 of 4 2 NM_175872.5 ENSP00000385099.1 Q3KQV3
ZNF792ENST00000605484.1 linkc.1660C>T p.Leu554Phe missense_variant Exon 2 of 2 1 ENSP00000474130.1 S4R3B8

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00000803
AC:
2
AN:
249220
AF XY:
0.0000149
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000291
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000545
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1460306
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
726248
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33460
American (AMR)
AF:
0.0000224
AC:
1
AN:
44574
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26056
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39680
South Asian (SAS)
AF:
0.00
AC:
0
AN:
85912
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53374
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5764
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1111174
Other (OTH)
AF:
0.00
AC:
0
AN:
60312
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.:
32
ExAC
AF:
0.0000165
AC:
2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.080
BayesDel_addAF
Benign
-0.46
T
BayesDel_noAF
Benign
-0.73
CADD
Benign
2.5
DANN
Benign
0.93
DEOGEN2
Benign
0.0074
T;T
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.0010
N
LIST_S2
Benign
0.34
T;T
M_CAP
Benign
0.0020
T
MetaRNN
Benign
0.042
T;T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
0.0
N;.
PhyloP100
0.015
PrimateAI
Benign
0.27
T
PROVEAN
Benign
-1.1
N;.
REVEL
Benign
0.0060
Sift
Benign
0.098
T;.
Sift4G
Benign
0.12
T;T
Polyphen
0.0050
B;.
Vest4
0.078
MutPred
0.31
Gain of methylation at K620 (P = 0.0263);.;
MVP
0.055
MPC
0.43
ClinPred
0.015
T
GERP RS
-1.8
Varity_R
0.028
gMVP
0.069
Mutation Taster
=99/1
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: rs747444990; hg19: chr19-35448898; API