Genetic Variant NAPG:c.56+32A>G (chr18-10526190-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003826.3(NAPG):c.56+32A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 1,504,230 control chromosomes in the GnomAD database, including 83,436 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 ( 8272 hom., cov: 31)

Exomes 𝑓: 0.34 ( 75164 hom. )

Consequence

NAPG
NM_003826.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.70

Publications

13 publications found

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:

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=-0.77).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAPG	NM_003826.3 link	c.56+32A>G		intron_variant	Intron 1 of 11	ENST00000322897.11	NP_003817.1	Q99747-1Q6FHY4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAPG	ENST00000322897.11 link	c.56+32A>G		intron_variant	Intron 1 of 11	1	NM_003826.3	ENSP00000324628.6		Q99747-1

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

49730

AN:

147940

Hom.:

8260

Cov.:

show subpopulations

Gnomad AFR

AF:

0.359

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.308

Gnomad ASJ

AF:

0.303

Gnomad EAS

AF:

0.436

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.330

Gnomad MID

AF:

0.328

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.325

GnomAD2 exomes

AF:

0.316

AC:

77557

AN:

245106

AF XY:

0.314

show subpopulations

Gnomad AFR exome

AF:

0.350

Gnomad AMR exome

AF:

0.273

Gnomad ASJ exome

AF:

0.316

Gnomad EAS exome

AF:

0.417

Gnomad FIN exome

AF:

0.316

Gnomad NFE exome

AF:

0.325

Gnomad OTH exome

AF:

0.323

GnomAD4 exome

AF:

0.342

AC:

464204

AN:

1356176

Hom.:

75164

Cov.:

AF XY:

0.341

AC XY:

229743

AN XY:

674180

show subpopulations

African (AFR)

AF:

0.384

AC:

11806

AN:

30726

American (AMR)

AF:

0.298

AC:

12389

AN:

41530

Ashkenazi Jewish (ASJ)

AF:

0.366

AC:

8150

AN:

22278

East Asian (EAS)

AF:

0.513

AC:

17383

AN:

33884

South Asian (SAS)

AF:

0.262

AC:

22201

AN:

84732

European-Finnish (FIN)

AF:

0.370

AC:

16575

AN:

44788

Middle Eastern (MID)

AF:

0.364

AC:

1605

AN:

4408

European-Non Finnish (NFE)

AF:

0.341

AC:

355253

AN:

1040318

Other (OTH)

AF:

0.352

AC:

18842

AN:

53512

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

15193

30386

45578

60771

75964

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11562

23124

34686

46248

57810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.336

AC:

49771

AN:

148054

Hom.:

8272

Cov.:

AF XY:

0.335

AC XY:

24206

AN XY:

72180

show subpopulations

African (AFR)

AF:

0.360

AC:

14598

AN:

40594

American (AMR)

AF:

0.307

AC:

4603

AN:

14980

Ashkenazi Jewish (ASJ)

AF:

0.303

AC:

1039

AN:

3426

East Asian (EAS)

AF:

0.435

AC:

2063

AN:

4744

South Asian (SAS)

AF:

0.293

AC:

1289

AN:

4398

European-Finnish (FIN)

AF:

0.330

AC:

3261

AN:

9894

Middle Eastern (MID)

AF:

0.337

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.327

AC:

21827

AN:

66746

Other (OTH)

AF:

0.323

AC:

673

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1704

3407

5111

6814

8518

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.330

Hom.:

2950

Bravo

AF:

0.330

Asia WGS

AF:

0.297

AC:

1028

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

5.3

(source)

DANN

Benign

0.80

PhyloP100

-1.7

PromoterAI

0.040

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over