Variant rs510110 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003826.3(NAPG):c.506+36A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 1,558,412 control chromosomes in the GnomAD database, including 93,854 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 0.34 ( 9049 hom., cov: 33)

Exomes 𝑓: 0.35 ( 84805 hom. )

Consequence

NAPG
NM_003826.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.607

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]

NAPG links:

NAPG (HGNC:):

NAPG links:

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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=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
NAPG	NM_003826.3 linkuse as main transcript	c.506+36A>C	intron_variant	ENST00000322897.11	NP_003817.1	Q99747-1Q6FHY4
NAPG	XM_011525754.3 linkuse as main transcript	c.686+36A>C	intron_variant		XP_011524056.1
NAPG	XM_011525756.3 linkuse as main transcript	c.260+36A>C	intron_variant		XP_011524058.1	Q99747-2
NAPG	XM_017026063.3 linkuse as main transcript	c.251+36A>C	intron_variant		XP_016881552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAPG	ENST00000322897.11 linkuse as main transcript	c.506+36A>C		intron_variant		1	NM_003826.3	ENSP00000324628.6		Q99747-1

Frequencies

GnomAD3 genomes

AF:

0.344

AC:

52270

AN:

151998

Hom.:

9044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.344

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.413

Gnomad SAS

AF:

0.293

Gnomad FIN

AF:

0.322

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.352

GnomAD3 exomes

AF:

0.341

AC:

80687

AN:

236844

Hom.:

14045

AF XY:

0.340

AC XY:

43715

AN XY:

128598

show subpopulations

Gnomad AFR exome

AF:

0.343

Gnomad AMR exome

AF:

0.294

Gnomad ASJ exome

AF:

0.352

Gnomad EAS exome

AF:

0.425

Gnomad SAS exome

AF:

0.293

Gnomad FIN exome

AF:

0.332

Gnomad NFE exome

AF:

0.353

Gnomad OTH exome

AF:

0.349

GnomAD4 exome

AF:

0.346

AC:

486069

AN:

1406296

Hom.:

84805

Cov.:

AF XY:

0.344

AC XY:

241518

AN XY:

701846

show subpopulations

Gnomad4 AFR exome

AF:

0.345

Gnomad4 AMR exome

AF:

0.296

Gnomad4 ASJ exome

AF:

0.345

Gnomad4 EAS exome

AF:

0.449

Gnomad4 SAS exome

AF:

0.292

Gnomad4 FIN exome

AF:

0.324

Gnomad4 NFE exome

AF:

0.349

Gnomad4 OTH exome

AF:

0.339

GnomAD4 genome

AF:

0.344

AC:

52287

AN:

152116

Hom.:

9049

Cov.:

AF XY:

0.342

AC XY:

25403

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.344

Gnomad4 AMR

AF:

0.322

Gnomad4 ASJ

AF:

0.328

Gnomad4 EAS

AF:

0.412

Gnomad4 SAS

AF:

0.294

Gnomad4 FIN

AF:

0.322

Gnomad4 NFE

AF:

0.350

Gnomad4 OTH

AF:

0.349

Alfa

AF:

0.284

Hom.:

1396

Bravo

AF:

0.344

Asia WGS

AF:

0.311

AC:

1080

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.38

DANN

Benign

0.71

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over