rs9962325

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003826.3(NAPG):​c.506+313C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 217,832 control chromosomes in the GnomAD database, including 1,965 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 0.087 ( 1821 hom., cov: 33)
Exomes 𝑓: 0.020 ( 144 hom. )

Consequence

NAPG
NM_003826.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.149
Variant links:
Genes affected
NAPG (HGNC:7642): (NSF attachment protein gamma) This gene encodes soluble NSF attachment protein gamma. The soluble NSF attachment proteins (SNAPs) enable N-ethyl-maleimide-sensitive fusion protein (NSF) to bind to target membranes. NSF and SNAPs appear to be general components of the intracellular membrane fusion apparatus, and their action at specific sites of fusion must be controlled by SNAP receptors particular to the membranes being fused. The product of this gene mediates platelet exocytosis and controls the membrane fusion events of this process.[provided by RefSeq, Dec 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NAPGNM_003826.3 linkuse as main transcriptc.506+313C>G intron_variant ENST00000322897.11
NAPGXM_011525754.3 linkuse as main transcriptc.686+313C>G intron_variant
NAPGXM_011525756.3 linkuse as main transcriptc.260+313C>G intron_variant
NAPGXM_017026063.3 linkuse as main transcriptc.251+313C>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAPGENST00000322897.11 linkuse as main transcriptc.506+313C>G intron_variant 1 NM_003826.3 P1Q99747-1

Frequencies

GnomAD3 genomes
AF:
0.0868
AC:
13189
AN:
152006
Hom.:
1811
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.292
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0328
Gnomad ASJ
AF:
0.0398
Gnomad EAS
AF:
0.0225
Gnomad SAS
AF:
0.0153
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.00210
Gnomad OTH
AF:
0.0617
GnomAD4 exome
AF:
0.0201
AC:
1318
AN:
65708
Hom.:
144
Cov.:
0
AF XY:
0.0186
AC XY:
624
AN XY:
33472
show subpopulations
Gnomad4 AFR exome
AF:
0.304
Gnomad4 AMR exome
AF:
0.0266
Gnomad4 ASJ exome
AF:
0.0374
Gnomad4 EAS exome
AF:
0.0220
Gnomad4 SAS exome
AF:
0.0124
Gnomad4 FIN exome
AF:
0.000603
Gnomad4 NFE exome
AF:
0.00205
Gnomad4 OTH exome
AF:
0.0337
GnomAD4 genome
AF:
0.0869
AC:
13227
AN:
152124
Hom.:
1821
Cov.:
33
AF XY:
0.0847
AC XY:
6299
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.292
Gnomad4 AMR
AF:
0.0327
Gnomad4 ASJ
AF:
0.0398
Gnomad4 EAS
AF:
0.0226
Gnomad4 SAS
AF:
0.0147
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.00210
Gnomad4 OTH
AF:
0.0611
Alfa
AF:
0.0578
Hom.:
129
Bravo
AF:
0.100
Asia WGS
AF:
0.0310
AC:
109
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
7.2
DANN
Benign
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9962325; hg19: chr18-10540709; API