chr19-53810081-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS2
The NM_144687.4(NLRP12):c.1578T>C(p.Tyr526Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
NLRP12
NM_144687.4 synonymous
NM_144687.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.83
Publications
0 publications found
Genes affected
NLRP12 (HGNC:22938): (NLR family pyrin domain containing 12) This gene encodes a member of the CATERPILLER family of cytoplasmic proteins. The encoded protein, which contains an N-terminal pyrin domain, a NACHT domain, a NACHT-associated domain, and a C-terminus leucine-rich repeat region, functions as an attenuating factor of inflammation by suppressing inflammatory responses in activated monocytes. Mutations in this gene cause familial cold autoinflammatory syndrome type 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]
NLRP12 Gene-Disease associations (from GenCC):
- familial cold autoinflammatory syndrome 2Inheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet, Laboratory for Molecular Medicine
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -9 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BP6
Variant 19-53810081-A-G is Benign according to our data. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-53810081-A-G is described in CliVar as Likely_benign. Clinvar id is 1932857.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.83 with no splicing effect.
BS2
High AC in GnomAdExome4 at 5 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLRP12 | ENST00000324134.11 | c.1578T>C | p.Tyr526Tyr | synonymous_variant | Exon 3 of 10 | 1 | NM_144687.4 | ENSP00000319377.6 | ||
NLRP12 | ENST00000345770.9 | c.1578T>C | p.Tyr526Tyr | synonymous_variant | Exon 3 of 9 | 1 | ENSP00000341428.5 | |||
NLRP12 | ENST00000391772.1 | c.1578T>C | p.Tyr526Tyr | synonymous_variant | Exon 3 of 7 | 1 | ENSP00000375652.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461892Hom.: 0 Cov.: 40 AF XY: 0.00000275 AC XY: 2AN XY: 727246 show subpopulations
GnomAD4 exome
AF:
AC:
5
AN:
1461892
Hom.:
Cov.:
40
AF XY:
AC XY:
2
AN XY:
727246
show subpopulations
African (AFR)
AF:
AC:
2
AN:
33480
American (AMR)
AF:
AC:
1
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53420
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1112010
Other (OTH)
AF:
AC:
0
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
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8
10
<30
30-35
35-40
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Age
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial cold autoinflammatory syndrome 2 Benign:1
Jun 19, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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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