6-87215909-C-T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_015021.3(ZNF292):​c.175C>T​(p.Leu59Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000692 in 1,445,526 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: 31)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

ZNF292
NM_015021.3 synonymous

Scores

1
4
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.48

Publications

0 publications found
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]
ZNF292 Gene-Disease associations (from GenCC):
  • complex neurodevelopmental disorder
    Inheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics, ClinGen
  • intellectual developmental disorder, autosomal dominant 64
    Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P

Genome browser will be placed here

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=0.15581924).
BP7
Synonymous conserved (PhyloP=2.48 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF292NM_015021.3 linkc.175C>T p.Leu59Leu synonymous_variant Exon 2 of 8 ENST00000369577.8 NP_055836.1 O60281-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF292ENST00000369577.8 linkc.175C>T p.Leu59Leu synonymous_variant Exon 2 of 8 1 NM_015021.3 ENSP00000358590.3 O60281-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
6.92e-7
AC:
1
AN:
1445526
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
719262
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
32206
American (AMR)
AF:
0.00
AC:
0
AN:
40400
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25494
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39018
South Asian (SAS)
AF:
0.00
AC:
0
AN:
83646
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53072
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5688
European-Non Finnish (NFE)
AF:
9.04e-7
AC:
1
AN:
1106436
Other (OTH)
AF:
0.00
AC:
0
AN:
59566
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
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.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.088
D
BayesDel_noAF
Benign
-0.11
CADD
Benign
14
DANN
Benign
0.91
DEOGEN2
Benign
0.0099
T
Eigen
Uncertain
0.26
Eigen_PC
Uncertain
0.32
FATHMM_MKL
Uncertain
0.78
D
LIST_S2
Benign
0.33
T
MetaRNN
Benign
0.16
T
MetaSVM
Benign
-0.95
T
PhyloP100
2.5
PROVEAN
Benign
-0.69
N
REVEL
Benign
0.022
Sift
Pathogenic
0.0
D
MutPred
0.23
Gain of MoRF binding (P = 0.0405);
MVP
0.35
ClinPred
0.44
T
GERP RS
4.8
Mutation Taster
=100/0
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs1772730013; hg19: chr6-87925627; API