11-7038634-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_176822.4(NLRP14):āc.48A>Gā(p.Leu16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000555 in 1,614,010 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: š 0.00053 ( 0 hom., cov: 32)
Exomes š: 0.00056 ( 6 hom. )
Consequence
NLRP14
NM_176822.4 synonymous
NM_176822.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.83
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant 11-7038634-A-G is Benign according to our data. Variant chr11-7038634-A-G is described in ClinVar as [Benign]. Clinvar id is 3048967.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-4.83 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000558 (816/1461824) while in subpopulation EAS AF= 0.0182 (722/39698). AF 95% confidence interval is 0.0171. There are 6 homozygotes in gnomad4_exome. There are 413 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLRP14 | NM_176822.4 | c.48A>G | p.Leu16= | synonymous_variant | 2/12 | ENST00000299481.5 | NP_789792.1 | |
NLRP14 | XM_011520044.2 | c.48A>G | p.Leu16= | synonymous_variant | 2/11 | XP_011518346.1 | ||
NLRP14 | XM_047426867.1 | c.48A>G | p.Leu16= | synonymous_variant | 2/11 | XP_047282823.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLRP14 | ENST00000299481.5 | c.48A>G | p.Leu16= | synonymous_variant | 2/12 | 5 | NM_176822.4 | ENSP00000299481 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000526 AC: 80AN: 152070Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00150 AC: 377AN: 251354Hom.: 4 AF XY: 0.00139 AC XY: 189AN XY: 135858
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GnomAD4 exome AF: 0.000558 AC: 816AN: 1461824Hom.: 6 Cov.: 32 AF XY: 0.000568 AC XY: 413AN XY: 727210
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GnomAD4 genome AF: 0.000526 AC: 80AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.000565 AC XY: 42AN XY: 74398
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
NLRP14-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 09, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at