chr11-114516108-C-T

Variant names:

• chr11-114516108-C-T
• rs561722
• XM_017017207.2:c.-639-1448C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017017207.2(NXPE2):​c.-639-1448C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,038 control chromosomes in the GnomAD database, including 9,587 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 0.35 (9587 hom., cov: 32)
• Consequence: NXPE2 XM_017017207.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 40 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 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: 0.349 AC: 53032 AN: 151920 Hom.: 9572 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.349 AC: 53083 AN: 152038 Hom.: 9587 Cov.: 32 AF XY: 0.353 AC XY: 26230 AN XY: 74294

African (AFR) AF: 0.315 AC: 13042 AN: 41436

American (AMR) AF: 0.328 AC: 5013 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3472

East Asian (EAS) AF: 0.655 AC: 3394 AN: 5180

South Asian (SAS) AF: 0.330 AC: 1586 AN: 4810

European-Finnish (FIN) AF: 0.399 AC: 4213 AN: 10566

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23656 AN: 67978

Other (OTH) AF: 0.340 AC: 718 AN: 2110

Alfa AF: 0.347 Hom.: 16097

Bravo AF: 0.344

Asia WGS AF: 0.469 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs561722; hg19: chr11-114386830;