rs543533

Positions:

• chr12-129016085-G-A
• chr12-129016085-G-C
• chr12-129016085-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000540920.1(NLRP9P1):​n.2077G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 361,168 control chromosomes in the GnomAD database, including 82,817 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.63 (31398 hom., cov: 32)
  • Exomes 𝑓: 0.69 (51419 hom.)
• Consequence: NLRP9P1 ENST00000540920.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

Genes affected

NLRP9P1 (HGNC:29888): (NLR family pyrin domain containing 9 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NLRP9P1		n.129016085G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NLRP9P1	ENST00000540920.1	n.2077G>A		non_coding_transcript_exon_variant	2/2	6

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95287 AN: 151994 Hom.: 31393 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.647

GnomAD4 exome AF: 0.694 AC: 145147 AN: 209056 Hom.: 51419 Cov.: 0 AF XY: 0.688 AC XY: 79893 AN XY: 116156

Gnomad4 AFR exome AF: 0.420

Gnomad4 AMR exome AF: 0.802

Gnomad4 ASJ exome AF: 0.665

Gnomad4 EAS exome AF: 0.932

Gnomad4 SAS exome AF: 0.626

Gnomad4 FIN exome AF: 0.761

Gnomad4 NFE exome AF: 0.691

Gnomad4 OTH exome AF: 0.691

GnomAD4 genome AF: 0.627 AC: 95328 AN: 152112 Hom.: 31398 Cov.: 32 AF XY: 0.635 AC XY: 47204 AN XY: 74356

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.652

Alfa AF: 0.686 Hom.: 71664

Bravo AF: 0.621

Asia WGS AF: 0.755 AC: 2623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs543533; hg19: chr12-129500630;