19-56004101-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_153447.4(NLRP5):c.442+6C>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00163 in 1,595,092 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0022 ( 10 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 47 hom. )
Consequence
NLRP5
NM_153447.4 splice_donor_region, intron
NM_153447.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00001041
2
Clinical Significance
Conservation
PhyloP100: 0.713
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 19-56004101-C-T is Benign according to our data. Variant chr19-56004101-C-T is described in ClinVar as [Benign]. Clinvar id is 713663.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0022 (335/152152) while in subpopulation EAS AF= 0.0445 (230/5166). AF 95% confidence interval is 0.0398. There are 10 homozygotes in gnomad4. There are 180 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP5 | NM_153447.4 | c.442+6C>T | splice_donor_region_variant, intron_variant | ENST00000390649.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP5 | ENST00000390649.8 | c.442+6C>T | splice_donor_region_variant, intron_variant | 1 | NM_153447.4 | P1 | |||
NLRP5 | ENST00000597673.1 | c.361+6C>T | splice_donor_region_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00221 AC: 336AN: 152034Hom.: 10 Cov.: 32
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GnomAD3 exomes AF: 0.00443 AC: 1038AN: 234050Hom.: 28 AF XY: 0.00399 AC XY: 505AN XY: 126498
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GnomAD4 exome AF: 0.00157 AC: 2268AN: 1442940Hom.: 47 Cov.: 32 AF XY: 0.00151 AC XY: 1082AN XY: 715698
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GnomAD4 genome AF: 0.00220 AC: 335AN: 152152Hom.: 10 Cov.: 32 AF XY: 0.00242 AC XY: 180AN XY: 74394
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at