rs10502192

Variant names:

• chr11-114751630-C-T
• rs10502192
• XM_017017211.2:c.1144+45634C>T

Variant summary

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

The XM_017017211.2(NXPE2):​c.1144+45634C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,864 control chromosomes in the GnomAD database, including 8,932 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 0.33 (8932 hom., cov: 31)
• Consequence: NXPE2 XM_017017211.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXPE2	XM_017017211.2	c.1144+45634C>T		intron_variant	Intron 5 of 5		XP_016872700.1
NXPE2	XM_017017212.2	c.1144+45634C>T		intron_variant	Intron 5 of 6		XP_016872701.1
NXPE2	XR_001747769.2	n.1277+11874C>T		intron_variant	Intron 6 of 6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49587 AN: 151746 Hom.: 8927 Cov.: 31

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.327 AC: 49609 AN: 151864 Hom.: 8932 Cov.: 31 AF XY: 0.328 AC XY: 24298 AN XY: 74182

African (AFR) AF: 0.171 AC: 7080 AN: 41396

American (AMR) AF: 0.378 AC: 5759 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3472

East Asian (EAS) AF: 0.427 AC: 2205 AN: 5166

South Asian (SAS) AF: 0.288 AC: 1384 AN: 4810

European-Finnish (FIN) AF: 0.382 AC: 4030 AN: 10542

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26610 AN: 67918

Other (OTH) AF: 0.336 AC: 709 AN: 2110

Alfa AF: 0.369 Hom.: 40316

Bravo AF: 0.324

Asia WGS AF: 0.343 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.57
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10502192; hg19: chr11-114622352;