5-150895451-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_052860.4(ZNF300):c.1788G>A(p.Gln596Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000435 in 1,608,952 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: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
ZNF300
NM_052860.4 synonymous
NM_052860.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.302
Publications
0 publications found
Genes affected
ZNF300 (HGNC:13091): (zinc finger protein 300) The protein encoded by this gene is a C2H2-type zinc finger DNA binding protein and likely transcriptional regulator. The function of this protein is not yet known. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2010]
IRGM (HGNC:29597): (immunity related GTPase M) This gene encodes a member of the p47 immunity-related GTPase family. The encoded protein may play a role in the innate immune response by regulating autophagy formation in response to intracellular pathogens. Polymorphisms that affect the normal expression of this gene are associated with a susceptibility to Crohn's disease and tuberculosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP7
Synonymous conserved (PhyloP=-0.302 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_052860.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZNF300 | MANE Select | c.1788G>A | p.Gln596Gln | synonymous | Exon 6 of 6 | NP_443092.1 | Q96RE9-1 | ||
| ZNF300 | c.1836G>A | p.Gln612Gln | synonymous | Exon 7 of 7 | NP_001166302.1 | Q96RE9-3 | |||
| ZNF300 | c.1680G>A | p.Gln560Gln | synonymous | Exon 5 of 5 | NP_001166303.1 | Q96RE9-4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZNF300 | TSL:1 MANE Select | c.1788G>A | p.Gln596Gln | synonymous | Exon 6 of 6 | ENSP00000274599.5 | Q96RE9-1 | ||
| ZNF300 | TSL:1 | c.1788G>A | p.Gln596Gln | synonymous | Exon 7 of 7 | ENSP00000397178.3 | Q96RE9-1 | ||
| IRGM | TSL:1 | n.*141-5138C>T | intron | N/A | ENSP00000429819.1 | A0A9H4B933 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152094Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152094
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
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Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
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GnomAD2 exomes AF: 0.0000201 AC: 5AN: 248782 AF XY: 0.0000298 show subpopulations
GnomAD2 exomes
AF:
AC:
5
AN:
248782
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.00000343 AC: 5AN: 1456740Hom.: 0 Cov.: 31 AF XY: 0.00000414 AC XY: 3AN XY: 724000 show subpopulations
GnomAD4 exome
AF:
AC:
5
AN:
1456740
Hom.:
Cov.:
31
AF XY:
AC XY:
3
AN XY:
724000
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33324
American (AMR)
AF:
AC:
3
AN:
44350
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25806
East Asian (EAS)
AF:
AC:
0
AN:
39582
South Asian (SAS)
AF:
AC:
1
AN:
85740
European-Finnish (FIN)
AF:
AC:
0
AN:
53240
Middle Eastern (MID)
AF:
AC:
0
AN:
5724
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1108826
Other (OTH)
AF:
AC:
0
AN:
60148
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.465
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
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0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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>80
Age
GnomAD4 genome 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74430 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152212
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
74430
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41560
American (AMR)
AF:
AC:
2
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5172
South Asian (SAS)
AF:
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10620
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67980
Other (OTH)
AF:
AC:
0
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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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