11-114479118-C-T

Variant names:

• chr11-114479118-C-T
• rs581015
• XM_017017209.2:c.-483+12169C>T

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+12169C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,102 control chromosomes in the GnomAD database, including 30,304 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 0.61 (30304 hom., cov: 32)
• Consequence: NXPE2 XM_017017209.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXPE2	XM_017017209.2	c.-483+12169C>T		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: 0.614 AC: 93257 AN: 151984 Hom.: 30250 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.614 AC: 93368 AN: 152102 Hom.: 30304 Cov.: 32 AF XY: 0.612 AC XY: 45483 AN XY: 74346

African (AFR) AF: 0.841 AC: 34932 AN: 41536

American (AMR) AF: 0.572 AC: 8736 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2074 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3139 AN: 5174

South Asian (SAS) AF: 0.569 AC: 2742 AN: 4818

European-Finnish (FIN) AF: 0.488 AC: 5158 AN: 10568

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34815 AN: 67946

Other (OTH) AF: 0.596 AC: 1257 AN: 2108

Alfa AF: 0.543 Hom.: 18147

Bravo AF: 0.629

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.80
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs581015; hg19: chr11-114349840;