chr11-7039746-A-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_176822.4(NLRP14):c.322A>T(p.Lys108*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00308 in 1,614,102 control chromosomes in the GnomAD database, including 136 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_176822.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLRP14 | NM_176822.4 | c.322A>T | p.Lys108* | stop_gained | Exon 3 of 12 | ENST00000299481.5 | NP_789792.1 | |
NLRP14 | XM_011520044.2 | c.322A>T | p.Lys108* | stop_gained | Exon 3 of 11 | XP_011518346.1 | ||
NLRP14 | XM_047426867.1 | c.322A>T | p.Lys108* | stop_gained | Exon 3 of 11 | XP_047282823.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00516 AC: 785AN: 152186Hom.: 19 Cov.: 32
GnomAD3 exomes AF: 0.0116 AC: 2908AN: 251302Hom.: 91 AF XY: 0.00867 AC XY: 1178AN XY: 135812
GnomAD4 exome AF: 0.00286 AC: 4181AN: 1461798Hom.: 117 Cov.: 30 AF XY: 0.00246 AC XY: 1787AN XY: 727212
GnomAD4 genome AF: 0.00517 AC: 788AN: 152304Hom.: 19 Cov.: 32 AF XY: 0.00577 AC XY: 430AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:3
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This variant is associated with the following publications: (PMID: 20981092, 22344438, 25525159, 16931801, 27535533) -
NLRP14-related disorder Benign:1
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 specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Spermatogenic Failure Benign:1
The heterozygous c.Lys108Ter variant in NLRP14 has been identified in an individual with azoospermia or severe oligozoospermia (PMID: 16931801), but has also been identified in >7% of Latino chromosomes and 34 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for autosomal recessive spermatogenic failure. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at