11-7070338-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_176822.4(NLRP14):c.3028C>T(p.Leu1010Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,608,730 control chromosomes in the GnomAD database, including 31,805 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_176822.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP14 | NM_176822.4 | c.3028C>T | p.Leu1010Phe | missense_variant | 11/12 | ENST00000299481.5 | |
NLRP14 | XM_011520044.2 | c.2857C>T | p.Leu953Phe | missense_variant | 10/11 | ||
NLRP14 | XM_047426867.1 | c.2857C>T | p.Leu953Phe | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP14 | ENST00000299481.5 | c.3028C>T | p.Leu1010Phe | missense_variant | 11/12 | 5 | NM_176822.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.152 AC: 23045AN: 152006Hom.: 2148 Cov.: 32
GnomAD3 exomes AF: 0.148 AC: 37184AN: 251174Hom.: 3336 AF XY: 0.151 AC XY: 20460AN XY: 135756
GnomAD4 exome AF: 0.194 AC: 282213AN: 1456606Hom.: 29657 Cov.: 29 AF XY: 0.192 AC XY: 139294AN XY: 725018
GnomAD4 genome AF: 0.152 AC: 23049AN: 152124Hom.: 2148 Cov.: 32 AF XY: 0.145 AC XY: 10795AN XY: 74376
ClinVar
Submissions by phenotype
NLRP14-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at