GeneBe

ENST00000521585.5:c.*18+15405C>T

Variant names:

Variant summary

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

The ENST00000521585.5(NSG2):​c.*18+15405C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,098 control chromosomes in the GnomAD database, including 6,545 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 0.29 ( 6545 hom., cov: 32)

Consequence

NSG2
ENST00000521585.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.595

Publications

2 publications found
Variant links:
Genes affected
NSG2 (HGNC:24955): (neuronal vesicle trafficking associated 2) Predicted to enable clathrin light chain binding activity. Predicted to be involved in clathrin coat assembly and endosomal transport. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

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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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NSG2ENST00000521585.5 linkc.*18+15405C>T intron_variant Intron 4 of 4 4 ENSP00000429863.1 E5RH73

Frequencies

GnomAD3 genomes
AF:
0.287
AC:
43632
AN:
151980
Hom.:
6539
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.219
Gnomad AMI
AF:
0.255
Gnomad AMR
AF:
0.341
Gnomad ASJ
AF:
0.237
Gnomad EAS
AF:
0.502
Gnomad SAS
AF:
0.280
Gnomad FIN
AF:
0.261
Gnomad MID
AF:
0.328
Gnomad NFE
AF:
0.307
Gnomad OTH
AF:
0.292
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.287
AC:
43654
AN:
152098
Hom.:
6545
Cov.:
32
AF XY:
0.287
AC XY:
21341
AN XY:
74330
show subpopulations
African (AFR)
AF:
0.218
AC:
9059
AN:
41494
American (AMR)
AF:
0.341
AC:
5215
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.237
AC:
822
AN:
3470
East Asian (EAS)
AF:
0.503
AC:
2598
AN:
5166
South Asian (SAS)
AF:
0.280
AC:
1349
AN:
4822
European-Finnish (FIN)
AF:
0.261
AC:
2764
AN:
10578
Middle Eastern (MID)
AF:
0.336
AC:
98
AN:
292
European-Non Finnish (NFE)
AF:
0.307
AC:
20900
AN:
67980
Other (OTH)
AF:
0.292
AC:
616
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1631
3261
4892
6522
8153
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
456
912
1368
1824
2280
<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:
0.304
Hom.:
12096
Bravo
AF:
0.294
Asia WGS
AF:
0.374
AC:
1297
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.92
DANN
Benign
0.60
PhyloP100
-0.59
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs4295404; hg19: chr5-173647712; API