11-7039128-AAGGAATTGAGTGAT-A

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.80
Variant links:
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]

Genome browser will be placed here

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
NLRP14NM_176822.4 linkuse as main transcriptc.289+262_289+275delAGTGATAGGAATTG intron_variant ENST00000299481.5 NP_789792.1 Q86W24
NLRP14XM_011520044.2 linkuse as main transcriptc.289+262_289+275delAGTGATAGGAATTG intron_variant XP_011518346.1
NLRP14XM_047426867.1 linkuse as main transcriptc.289+262_289+275delAGTGATAGGAATTG intron_variant XP_047282823.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NLRP14ENST00000299481.5 linkuse as main transcriptc.289+262_289+275delAGTGATAGGAATTG intron_variant 5 NM_176822.4 ENSP00000299481.5 Q86W24

Frequencies

GnomAD3 genomes
AF:
0.151
AC:
22938
AN:
151918
Hom.:
2145
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.0808
Gnomad AMI
AF:
0.240
Gnomad AMR
AF:
0.151
Gnomad ASJ
AF:
0.200
Gnomad EAS
AF:
0.0145
Gnomad SAS
AF:
0.0856
Gnomad FIN
AF:
0.0964
Gnomad MID
AF:
0.190
Gnomad NFE
AF:
0.212
Gnomad OTH
AF:
0.184
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.151
AC:
22942
AN:
152036
Hom.:
2145
Cov.:
27
AF XY:
0.144
AC XY:
10731
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.0808
Gnomad4 AMR
AF:
0.151
Gnomad4 ASJ
AF:
0.200
Gnomad4 EAS
AF:
0.0147
Gnomad4 SAS
AF:
0.0861
Gnomad4 FIN
AF:
0.0964
Gnomad4 NFE
AF:
0.212
Gnomad4 OTH
AF:
0.181
Alfa
AF:
0.179
Hom.:
299
Bravo
AF:
0.154
Asia WGS
AF:
0.0550
AC:
190
AN:
3478

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 submitterclinical testingGeneDxJun 21, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs60100976; hg19: chr11-7060359; API