19-54939682-C-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001127255.2(NLRP7):c.1137G>C(p.Lys379Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,612,818 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. K379K) has been classified as Benign.
Frequency
Consequence
NM_001127255.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLRP7 | NM_001127255.2 | c.1137G>C | p.Lys379Asn | missense_variant | Exon 4 of 11 | NP_001120727.1 | ||
NLRP7 | NM_001405531.1 | c.1137G>C | p.Lys379Asn | missense_variant | Exon 6 of 13 | NP_001392460.1 | ||
NLRP7 | NM_139176.4 | c.1137G>C | p.Lys379Asn | missense_variant | Exon 4 of 11 | NP_631915.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00389 AC: 591AN: 151890Hom.: 12 Cov.: 31
GnomAD3 exomes AF: 0.00501 AC: 1248AN: 249060Hom.: 20 AF XY: 0.00483 AC XY: 652AN XY: 135116
GnomAD4 exome AF: 0.00225 AC: 3290AN: 1460810Hom.: 55 Cov.: 74 AF XY: 0.00226 AC XY: 1639AN XY: 726734
GnomAD4 genome AF: 0.00389 AC: 591AN: 152008Hom.: 12 Cov.: 31 AF XY: 0.00585 AC XY: 435AN XY: 74306
ClinVar
Submissions by phenotype
Hydatidiform mole, recurrent, 1 Uncertain:1Other:1
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
not provided Benign:1
NLRP7: BP4, BS1, BS2 -
Malignant tumor of prostate Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at