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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXPE2	XM_017017209.2	c.-483+6239A>G		intron_variant	Intron 1 of 10		XP_016872698.1

Ensembl

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

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 v4.3

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;