XM_017017207.2:c.-47+20474A>G

Variant names:

• chr11-114561234-A-G
• rs678170
• XM_017017207.2:c.-47+20474A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.552 AC: 22881 AN: 41442

American (AMR) AF: 0.359 AC: 5493 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1201 AN: 3466

East Asian (EAS) AF: 0.664 AC: 3413 AN: 5142

South Asian (SAS) AF: 0.329 AC: 1588 AN: 4822

European-Finnish (FIN) AF: 0.391 AC: 4139 AN: 10574

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23611 AN: 67944

Other (OTH) AF: 0.394 AC: 830 AN: 2106

Alfa AF: 0.359 Hom.: 13968

Bravo AF: 0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.7
DANN	Benign	0.89
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs678170; hg19: chr11-114431956;