chr12-129016085-G-A

Variant names:

• chr12-129016085-G-A
• rs543533
• ENST00000540920.1:n.2077G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540920.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NLRP9P1	ENST00000540920.1	TSL:6	n.2077G>A		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 0.420 AC: 2359 AN: 5614

American (AMR) AF: 0.802 AC: 10713 AN: 13356

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 3068 AN: 4614

East Asian (EAS) AF: 0.932 AC: 9266 AN: 9942

South Asian (SAS) AF: 0.626 AC: 23132 AN: 36948

European-Finnish (FIN) AF: 0.761 AC: 11180 AN: 14700

Middle Eastern (MID) AF: 0.577 AC: 828 AN: 1434

European-Non Finnish (NFE) AF: 0.691 AC: 77620 AN: 112352

Other (OTH) AF: 0.691 AC: 6981 AN: 10096

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

African (AFR) AF: 0.410 AC: 16992 AN: 41494

American (AMR) AF: 0.734 AC: 11223 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2240 AN: 3466

East Asian (EAS) AF: 0.916 AC: 4737 AN: 5174

South Asian (SAS) AF: 0.638 AC: 3073 AN: 4818

European-Finnish (FIN) AF: 0.755 AC: 7973 AN: 10560

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46973 AN: 68002

Other (OTH) AF: 0.652 AC: 1372 AN: 2104

Alfa AF: 0.677 Hom.: 150261

Bravo AF: 0.621

Asia WGS AF: 0.755 AC: 2623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.51
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs543533; hg19: chr12-129500630;