11-114561234-A-G

Position:

• chr11-114561234-A-G

Variant summary

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

The XM_017017207.2(NXPE2):​c.-47+20474A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,982 control chromosomes in the GnomAD database, including 14,010 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 0.42 (14010 hom., cov: 32)
• Consequence: NXPE2 XM_017017207.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

Genes affected

NXPE2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NXPE2	XM_017017207.2	c.-47+20474A>G		intron_variant			XP_016872696.1
NXPE2	XM_017017209.2	c.-47+20474A>G		intron_variant			XP_016872698.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63329 AN: 151864 Hom.: 13987 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.417 AC: 63405 AN: 151982 Hom.: 14010 Cov.: 32 AF XY: 0.420 AC XY: 31173 AN XY: 74280

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.394

Alfa AF: 0.356 Hom.: 3303

Bravo AF: 0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.7
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs678170; hg19: chr11-114431956;