rs973945684
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_015021.3(ZNF292):c.118C>A(p.Arg40Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000208 in 1,444,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
ZNF292
NM_015021.3 synonymous
NM_015021.3 synonymous
Scores
1
2
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.525
Publications
0 publications found
Genes affected
ZNF292 (HGNC:18410): (zinc finger protein 292) This gene encodes a growth hormone-dependent, zinc finger transcription factor that functions as a tumor suppressor. Naturally occurring mutations in this gene are associated with gastric cancer, colorectal cancer, and chronic lymphocytic leukemia. [provided by RefSeq, May 2017]
ZNF292 Gene-Disease associations (from GenCC):
- complex neurodevelopmental disorderInheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics, ClinGen
- intellectual developmental disorder, autosomal dominant 64Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08680183).
BP7
Synonymous conserved (PhyloP=0.525 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ZNF292 | NM_015021.3 | c.118C>A | p.Arg40Arg | synonymous_variant | Exon 1 of 8 | ENST00000369577.8 | NP_055836.1 | |
| ZNF292 | NM_001351444.2 | c.-448C>A | 5_prime_UTR_variant | Exon 1 of 9 | NP_001338373.1 | |||
| ZNF292 | XM_047418459.1 | c.-616C>A | 5_prime_UTR_variant | Exon 1 of 10 | XP_047274415.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000208 AC: 3AN: 1444612Hom.: 0 Cov.: 31 AF XY: 0.00000418 AC XY: 3AN XY: 717012 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1444612
Hom.:
Cov.:
31
AF XY:
AC XY:
3
AN XY:
717012
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33194
American (AMR)
AF:
AC:
0
AN:
42718
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25692
East Asian (EAS)
AF:
AC:
0
AN:
39092
South Asian (SAS)
AF:
AC:
0
AN:
83574
European-Finnish (FIN)
AF:
AC:
0
AN:
51010
Middle Eastern (MID)
AF:
AC:
0
AN:
4222
European-Non Finnish (NFE)
AF:
AC:
3
AN:
1105514
Other (OTH)
AF:
AC:
0
AN:
59596
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
PhyloP100
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
MutPred
Gain of MoRF binding (P = 0.052);
MVP
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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