XM_017017209.2:c.-483+6239A>G

Variant names:

• chr11-114473188-A-G
• rs10502189
• XM_017017209.2:c.-483+6239A>G

Variant summary

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

The XM_017017209.2(NXPE2):​c.-483+6239A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0757 in 152,252 control chromosomes in the GnomAD database, including 615 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 0.076 (615 hom., cov: 32)
• Consequence: NXPE2 XM_017017209.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 6 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0757 AC: 11522 AN: 152134 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.0568

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.0622

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0757 AC: 11531 AN: 152252 Hom.: 615 Cov.: 32 AF XY: 0.0803 AC XY: 5979 AN XY: 74426

African (AFR) AF: 0.0566 AC: 2355 AN: 41574

American (AMR) AF: 0.0454 AC: 695 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0729 AC: 253 AN: 3472

East Asian (EAS) AF: 0.230 AC: 1187 AN: 5170

South Asian (SAS) AF: 0.0641 AC: 309 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1832 AN: 10580

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0696 AC: 4731 AN: 68016

Other (OTH) AF: 0.0634 AC: 134 AN: 2114

Alfa AF: 0.0682 Hom.: 1199

Bravo AF: 0.0648

Asia WGS AF: 0.120 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.85
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10502189; hg19: chr11-114343910;