rs1792379

Variant names:

• chr11-114756897-G-A
• rs1792379
• XM_017017211.2:c.1145-47885G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001747769.2(NXPE2):​n.1277+17141G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,938 control chromosomes in the GnomAD database, including 17,455 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 0.47 (17455 hom., cov: 30)
• Consequence: NXPE2 XR_001747769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 7 publications found

Genes affected

NXPE2 (HGNC:26331): (neurexophilin and PC-esterase domain family member 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71458 AN: 151820 Hom.: 17449 Cov.: 30

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.491

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.471 AC: 71496 AN: 151938 Hom.: 17455 Cov.: 30 AF XY: 0.476 AC XY: 35312 AN XY: 74244

African (AFR) AF: 0.351 AC: 14539 AN: 41430

American (AMR) AF: 0.484 AC: 7388 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1786 AN: 3466

East Asian (EAS) AF: 0.508 AC: 2616 AN: 5150

South Asian (SAS) AF: 0.599 AC: 2868 AN: 4790

European-Finnish (FIN) AF: 0.549 AC: 5794 AN: 10560

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35074 AN: 67952

Other (OTH) AF: 0.492 AC: 1039 AN: 2110

Alfa AF: 0.505 Hom.: 17602

Bravo AF: 0.456

Asia WGS AF: 0.550 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.48
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1792379; hg19: chr11-114627619;