Genetic Variant NM_003826.3:c.506+313C>G (chr18-10540712-C-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.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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.149

Publications

1 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:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003826.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAPG	NM_003826.3	MANE Select	c.506+313C>G		intron	N/A	NP_003817.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NAPG	ENST00000322897.11	TSL:1 MANE Select	c.506+313C>G	intron	N/A	ENSP00000324628.6
NAPG	ENST00000582978.5	TSL:2	n.820C>G	non_coding_transcript_exon	Exon 8 of 8
NAPG	ENST00000580224.5	TSL:2	n.*369+313C>G	intron	N/A	ENSP00000463265.1

Frequencies

GnomAD3 genomes

AF:

0.0868

AC:

13189

AN:

152006

Hom.:

1811

Cov.:

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.:

AF XY:

0.0186

AC XY:

624

AN XY:

33472

show subpopulations

African (AFR)

AF:

0.304

AC:

773

AN:

2542

American (AMR)

AF:

0.0266

AC:

AN:

2252

Ashkenazi Jewish (ASJ)

AF:

0.0374

AC:

AN:

2648

East Asian (EAS)

AF:

0.0220

AC:

110

AN:

4990

South Asian (SAS)

AF:

0.0124

AC:

AN:

1128

European-Finnish (FIN)

AF:

0.000603

AC:

AN:

3316

Middle Eastern (MID)

AF:

0.0357

AC:

AN:

336

European-Non Finnish (NFE)

AF:

0.00205

AC:

AN:

43804

Other (OTH)

AF:

0.0337

AC:

158

AN:

4692

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

106

160

213

266

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0869

AC:

13227

AN:

152124

Hom.:

1821

Cov.:

AF XY:

0.0847

AC XY:

6299

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.292

AC:

12116

AN:

41432

American (AMR)

AF:

0.0327

AC:

500

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0398

AC:

138

AN:

3470

East Asian (EAS)

AF:

0.0226

AC:

117

AN:

5186

South Asian (SAS)

AF:

0.0147

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.000377

AC:

AN:

10600

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00210

AC:

143

AN:

68012

Other (OTH)

AF:

0.0611

AC:

129

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

475

950

1424

1899

2374

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<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:

0.0578

Hom.:

129

Bravo

AF:

0.100

Asia WGS

AF:

0.0310

AC:

109

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.2

(source)

DANN

Benign

0.58

PhyloP100

-0.15

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over