chr11-7960043-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001391958.1(NLRP10):c.1569A>T(p.Lys523Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,092 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001391958.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP10 | NM_001391958.1 | c.1569A>T | p.Lys523Asn | missense_variant | 3/3 | ENST00000691676.1 | |
NLRP10 | NM_176821.4 | c.1569A>T | p.Lys523Asn | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP10 | ENST00000691676.1 | c.1569A>T | p.Lys523Asn | missense_variant | 3/3 | NM_001391958.1 | P1 | ||
NLRP10 | ENST00000328600.3 | c.1569A>T | p.Lys523Asn | missense_variant | 2/2 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251452Hom.: 1 AF XY: 0.0000221 AC XY: 3AN XY: 135914
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461834Hom.: 1 Cov.: 34 AF XY: 0.00000963 AC XY: 7AN XY: 727224
GnomAD4 genome AF: 0.000112 AC: 17AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2024 | The c.1569A>T (p.K523N) alteration is located in exon 2 (coding exon 2) of the NLRP10 gene. This alteration results from a A to T substitution at nucleotide position 1569, causing the lysine (K) at amino acid position 523 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at