GeneBe

rs5862

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001162371.3(LOC728392):​c.*880T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

LOC728392
NM_001162371.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.536

Publications

27 publications found
Variant links:
Genes affected
NLRP1 (HGNC:14374): (NLR family pyrin domain containing 1) This gene encodes a member of the Ced-4 family of apoptosis proteins. Ced-family members contain a caspase recruitment domain (CARD) and are known to be key mediators of programmed cell death. The encoded protein contains a distinct N-terminal pyrin-like motif, which is possibly involved in protein-protein interactions. This protein interacts strongly with caspase 2 and weakly with caspase 9. Overexpression of this gene was demonstrated to induce apoptosis in cells. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]
NLRP1 Gene-Disease associations (from GenCC):
  • corneal intraepithelial dyskeratosis-palmoplantar hyperkeratosis-laryngeal dyskeratosis syndrome
    Inheritance: AD, SD Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
  • autoinflammation with arthritis and dyskeratosis
    Inheritance: AR, SD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001162371.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
LOC728392
NM_001162371.3
MANE Select
c.*880T>G
3_prime_UTR
Exon 2 of 2NP_001155843.1A0A494C1I1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ENSG00000286190
ENST00000568641.2
TSL:1 MANE Select
c.*880T>G
3_prime_UTR
Exon 2 of 2ENSP00000499042.1A0A494C1I1
NLRP1
ENST00000699801.1
c.*66T>G
3_prime_UTR
Exon 3 of 3ENSP00000514604.1A0A8V8TQK4
NLRP1
ENST00000699800.1
c.*66T>G
3_prime_UTR
Exon 2 of 2ENSP00000514603.1A0A8V8TPB4

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
230518
Hom.:
0
Cov.:
5
AF XY:
0.00
AC XY:
0
AN XY:
109408
African (AFR)
AF:
0.00
AC:
0
AN:
4460
American (AMR)
AF:
0.00
AC:
0
AN:
288
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
1436
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1018
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4812
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
72
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
484
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
210266
Other (OTH)
AF:
0.00
AC:
0
AN:
7682
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
3.1
DANN
Benign
0.19
PhyloP100
-0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs5862; hg19: chr17-5402957; API