19-56008716-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_153447.4(NLRP5):c.443-72C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000172 in 1,334,230 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00018 ( 2 hom. )
Consequence
NLRP5
NM_153447.4 intron
NM_153447.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.70
Genes affected
NLRP5 (HGNC:21269): (NLR family pyrin domain containing 5) 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). Expression of this gene is restricted to the oocyte. A mouse gene that encodes a maternal oocyte protein, similar to this encoded protein, is required for normal early embryogenesis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000125 (19/152256) while in subpopulation EAS AF= 0.00232 (12/5176). AF 95% confidence interval is 0.00134. There are 0 homozygotes in gnomad4. There are 11 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP5 | NM_153447.4 | c.443-72C>T | intron_variant | ENST00000390649.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP5 | ENST00000390649.8 | c.443-72C>T | intron_variant | 1 | NM_153447.4 | P1 | |||
NLRP5 | ENST00000597673.1 | c.362-72C>T | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152138Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000179 AC: 211AN: 1181974Hom.: 2 AF XY: 0.000190 AC XY: 113AN XY: 593390
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GnomAD4 genome AF: 0.000125 AC: 19AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74450
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not provided Other:1
not provided, no classification provided | literature only | Human Evolutionary Genetics, Institut Pasteur | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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