19-54939682-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001127255.2(NLRP7):c.1137G>A(p.Lys379Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,612,666 control chromosomes in the GnomAD database, including 36,759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001127255.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLRP7 | NM_001127255.2 | c.1137G>A | p.Lys379Lys | synonymous_variant | Exon 4 of 11 | NP_001120727.1 | ||
NLRP7 | NM_001405531.1 | c.1137G>A | p.Lys379Lys | synonymous_variant | Exon 6 of 13 | NP_001392460.1 | ||
NLRP7 | NM_139176.4 | c.1137G>A | p.Lys379Lys | synonymous_variant | Exon 4 of 11 | NP_631915.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.189 AC: 28674AN: 151800Hom.: 2948 Cov.: 31
GnomAD3 exomes AF: 0.212 AC: 52890AN: 249060Hom.: 5921 AF XY: 0.211 AC XY: 28555AN XY: 135116
GnomAD4 exome AF: 0.213 AC: 311722AN: 1460750Hom.: 33807 Cov.: 74 AF XY: 0.213 AC XY: 154719AN XY: 726708
GnomAD4 genome AF: 0.189 AC: 28688AN: 151916Hom.: 2952 Cov.: 31 AF XY: 0.191 AC XY: 14213AN XY: 74254
ClinVar
Submissions by phenotype
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 -
Hydatidiform mole, recurrent, 1 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at