11-7039128-AAGGAATTGAGTGAT-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_176822.4(NLRP14):c.289+262_289+275delAGTGATAGGAATTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,036 control chromosomes in the GnomAD database, including 2,145 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.15 ( 2145 hom., cov: 27)
Consequence
NLRP14
NM_176822.4 intron
NM_176822.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.80
Genes affected
NLRP14 (HGNC:22939): (NLR family pyrin domain containing 14) The protein encoded by this gene belongs to the NALP protein family. 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). This protein may play a regulatory role in the innate immune system as similar family members belong to the signal-induced multiprotein complex, the inflammasome, that activates the pro-inflammatory caspases, caspase-1 and caspase-5. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 11-7039128-AAGGAATTGAGTGAT-A is Benign according to our data. Variant chr11-7039128-AAGGAATTGAGTGAT-A is described in ClinVar as [Benign]. Clinvar id is 1235606.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLRP14 | NM_176822.4 | c.289+262_289+275delAGTGATAGGAATTG | intron_variant | ENST00000299481.5 | NP_789792.1 | |||
NLRP14 | XM_011520044.2 | c.289+262_289+275delAGTGATAGGAATTG | intron_variant | XP_011518346.1 | ||||
NLRP14 | XM_047426867.1 | c.289+262_289+275delAGTGATAGGAATTG | intron_variant | XP_047282823.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLRP14 | ENST00000299481.5 | c.289+262_289+275delAGTGATAGGAATTG | intron_variant | 5 | NM_176822.4 | ENSP00000299481.5 |
Frequencies
GnomAD3 genomes AF: 0.151 AC: 22938AN: 151918Hom.: 2145 Cov.: 27
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.151 AC: 22942AN: 152036Hom.: 2145 Cov.: 27 AF XY: 0.144 AC XY: 10731AN XY: 74338
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190
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 21, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at