11-114756897-G-A

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 XM_017017211.2(NXPE2):​c.1145-47885G>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 XM_017017211.2 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXPE2	XM_017017211.2	c.1145-47885G>A		intron_variant	Intron 5 of 5		XP_016872700.1
NXPE2	XM_017017212.2	c.1145-47885G>A		intron_variant	Intron 5 of 6		XP_016872701.1
NXPE2	XR_001747769.2	n.1277+17141G>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;