chr11-7960275-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001391958.1(NLRP10):āc.1337T>Cā(p.Phe446Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00041 in 1,614,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00034 ( 0 hom., cov: 32)
Exomes š: 0.00042 ( 0 hom. )
Consequence
NLRP10
NM_001391958.1 missense
NM_001391958.1 missense
Scores
6
9
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.03
Genes affected
NLRP10 (HGNC:21464): (NLR family pyrin domain containing 10) Members of the NALP protein family typically contain a NACHT domain, a NACHT-associated domain (NAD), a C-terminal leucine-rich repeat (LRR) region, and an N-terminal pyrin domain (PYD). The protein encoded by this gene belongs to the NALP protein family despite lacking the LRR region. This protein likely plays a regulatory role in the innate immune system. The protein belongs to the signal-induced multiprotein complex, the inflammasome, that activates the pro-inflammatory caspases, caspase-1 and caspase-5. Other experiments indicate that this gene acts as a multifunctional negative regulator of inflammation and apoptosis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.75
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP10 | NM_001391958.1 | c.1337T>C | p.Phe446Ser | missense_variant | 3/3 | ENST00000691676.1 | |
NLRP10 | NM_176821.4 | c.1337T>C | p.Phe446Ser | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP10 | ENST00000691676.1 | c.1337T>C | p.Phe446Ser | missense_variant | 3/3 | NM_001391958.1 | P1 | ||
NLRP10 | ENST00000328600.3 | c.1337T>C | p.Phe446Ser | missense_variant | 2/2 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152142Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000426 AC: 107AN: 251446Hom.: 0 AF XY: 0.000412 AC XY: 56AN XY: 135896
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GnomAD4 exome AF: 0.000417 AC: 609AN: 1461876Hom.: 0 Cov.: 34 AF XY: 0.000384 AC XY: 279AN XY: 727238
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GnomAD4 genome AF: 0.000342 AC: 52AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74320
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
M
MutationTaster
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
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MPC
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T
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at