GeneBe

XM_017017207.2:c.-639-1448C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.438

Publications

40 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NXPE2XM_017017207.2 linkc.-639-1448C>T intron_variant Intron 1 of 11 XP_016872696.1
NXPE2XM_017017209.2 linkc.-482-10515C>T intron_variant Intron 1 of 10 XP_016872698.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.349
AC:
53032
AN:
151920
Hom.:
9572
Cov.:
32
show subpopulations
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
show subpopulations
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
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1749
3497
5246
6994
8743
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
522
1044
1566
2088
2610
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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 v4.3

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

Publications

Other links and lift over

dbSNP: rs561722; hg19: chr11-114386830; API