6-87155670-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000369577.8(ZNF292):​c.79G>C​(p.Glu27Gln) 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: 33)

Consequence

ZNF292
ENST00000369577.8 missense

Scores

3
6
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.43
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2314687).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZNF292NM_015021.3 linkuse as main transcriptc.79G>C p.Glu27Gln missense_variant 1/8 ENST00000369577.8 NP_055836.1
ZNF292NM_001351444.2 linkuse as main transcriptc.-487G>C 5_prime_UTR_variant 1/9 NP_001338373.1
ZNF292XM_047418459.1 linkuse as main transcriptc.-655G>C 5_prime_UTR_variant 1/10 XP_047274415.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZNF292ENST00000369577.8 linkuse as main transcriptc.79G>C p.Glu27Gln missense_variant 1/81 NM_015021.3 ENSP00000358590 P1O60281-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGeneDxFeb 21, 2023Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.075
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
23
DANN
Uncertain
0.98
DEOGEN2
Benign
0.077
T;T;T;T
Eigen
Uncertain
0.24
Eigen_PC
Uncertain
0.32
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Benign
0.80
T;T;T;T
M_CAP
Uncertain
0.20
D
MetaRNN
Benign
0.23
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.3
.;L;.;.
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Pathogenic
0.80
T
PROVEAN
Uncertain
-2.5
D;N;N;N
REVEL
Benign
0.024
Sift
Pathogenic
0.0
D;T;D;T
Sift4G
Pathogenic
0.0
D;T;D;T
Polyphen
0.17
.;B;.;.
Vest4
0.31
MutPred
0.14
Gain of MoRF binding (P = 0.057);Gain of MoRF binding (P = 0.057);Gain of MoRF binding (P = 0.057);Gain of MoRF binding (P = 0.057);
MVP
0.043
ClinPred
0.86
D
GERP RS
4.5
RBP_binding_hub_radar
0.97
RBP_regulation_power_radar
2.7
Varity_R
0.24
gMVP
0.28

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-87865388; API