4-112540943-T-C
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_018392.5(ZGRF1):c.5788A>G(p.Asn1930Asp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ZGRF1
NM_018392.5 missense
NM_018392.5 missense
Scores
10
7
Clinical Significance
Conservation
PhyloP100: 3.73
Publications
0 publications found
Genes affected
ZGRF1 (HGNC:25654): (zinc finger GRF-type containing 1) The encoded protein contains GRF zinc finger (zf-GRF) and transmembrane domains. GRF zinc fingers are found in a number of DNA-binding proteins. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.4109727).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_018392.5. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZGRF1 | TSL:5 MANE Select | c.5788A>G | p.Asn1930Asp | missense | Exon 26 of 28 | ENSP00000424737.1 | Q86YA3-1 | ||
| ZGRF1 | TSL:5 | c.5788A>G | p.Asn1930Asp | missense | Exon 25 of 27 | ENSP00000390505.3 | Q86YA3-1 | ||
| ZGRF1 | c.5614A>G | p.Asn1872Asp | missense | Exon 25 of 27 | ENSP00000595990.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00 AC: 0AN: 182582 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
182582
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1416012Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 700094
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1416012
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
700094
African (AFR)
AF:
AC:
0
AN:
32544
American (AMR)
AF:
AC:
0
AN:
37694
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25436
East Asian (EAS)
AF:
AC:
0
AN:
37790
South Asian (SAS)
AF:
AC:
0
AN:
80836
European-Finnish (FIN)
AF:
AC:
0
AN:
50516
Middle Eastern (MID)
AF:
AC:
0
AN:
5708
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1086780
Other (OTH)
AF:
AC:
0
AN:
58708
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Uncertain
D
MutationAssessor
Benign
N
PhyloP100
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Vest4
MutPred
Gain of disorder (P = 0.1216)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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