rs7949181

Positions:

• chr11-114794390-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017017211.2(NXPE2):​c.1145-10392T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,094 control chromosomes in the GnomAD database, including 5,960 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 0.28 (5960 hom., cov: 32)
• Consequence: NXPE2 XM_017017211.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NXPE2	XM_017017211.2	c.1145-10392T>C		intron_variant			XP_016872700.1
NXPE2	XM_017017212.2	c.1145-10392T>C		intron_variant			XP_016872701.1
		n.114794390T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41942 AN: 151976 Hom.: 5933 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.276 AC: 42021 AN: 152094 Hom.: 5960 Cov.: 32 AF XY: 0.281 AC XY: 20882 AN XY: 74338

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.271

Alfa AF: 0.250 Hom.: 6760

Bravo AF: 0.283

Asia WGS AF: 0.317 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7949181; hg19: chr11-114665112;