18-10549365-C-A

Variant names:

• chr18-10549365-C-A
• rs617040
• NM_003826.3:c.795+269C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003826.3(NAPG):​c.795+269C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,038 control chromosomes in the GnomAD database, including 27,157 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 0.58 (27157 hom., cov: 32)
• Consequence: NAPG NM_003826.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAPG	NM_003826.3	c.795+269C>A		intron_variant	Intron 11 of 11	ENST00000322897.11	NP_003817.1
NAPG	XM_011525754.3	c.975+269C>A		intron_variant	Intron 12 of 12		XP_011524056.1
NAPG	XM_011525756.3	c.549+269C>A		intron_variant	Intron 9 of 9		XP_011524058.1
NAPG	XM_017026063.3	c.540+269C>A		intron_variant	Intron 7 of 7		XP_016881552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAPG	ENST00000322897.11	c.795+269C>A		intron_variant	Intron 11 of 11	1	NM_003826.3	ENSP00000324628.6
NAPG	ENST00000580224.5	n.*658+269C>A		intron_variant	Intron 10 of 10	2		ENSP00000463265.1
NAPG	ENST00000580483.5	n.*536+269C>A		intron_variant	Intron 7 of 7	3		ENSP00000464496.1
NAPG	ENST00000583367.1	n.1175+269C>A		intron_variant	Intron 6 of 6	2

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87478 AN: 151920 Hom.: 27117 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.542

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.576 AC: 87569 AN: 152038 Hom.: 27157 Cov.: 32 AF XY: 0.570 AC XY: 42371 AN XY: 74282

African (AFR) AF: 0.819 AC: 34007 AN: 41502

American (AMR) AF: 0.486 AC: 7422 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1629 AN: 3470

East Asian (EAS) AF: 0.676 AC: 3492 AN: 5166

South Asian (SAS) AF: 0.470 AC: 2260 AN: 4812

European-Finnish (FIN) AF: 0.446 AC: 4704 AN: 10544

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32234 AN: 67958

Other (OTH) AF: 0.537 AC: 1135 AN: 2112

Alfa AF: 0.564 Hom.: 3721

Bravo AF: 0.594

Asia WGS AF: 0.532 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.056
DANN	Benign	0.36
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs617040; hg19: chr18-10549362;