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 XR_001747769.2(NXPE2):​n.1277+11874C>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 XR_001747769.2 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.

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: 0.327 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 v4.9

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;