chr11-114479118-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.

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: 0.614 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 v4.9

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;