rs2290279

chr18-10526190-A-Gchr18-10526190-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NAPG	NM_003826.3	c.56+32A>G		intron_variant		ENST00000322897.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAPG	ENST00000322897.11	c.56+32A>G		intron_variant		1	NM_003826.3	P1

Frequencies

GnomAD3 genomes AF: 0.336 AC: 49730 AN: 147940 Hom.: 8260 Cov.: 31

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

GnomAD3 exomes AF: 0.316 AC: 77557 AN: 245106 Hom.: 12705 AF XY: 0.314 AC XY: 41892 AN XY: 133384

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 SAS exome AF: 0.256

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.: 28 AF XY: 0.341 AC XY: 229743 AN XY: 674180

Gnomad4 AFR exome AF: 0.384

Gnomad4 AMR exome AF: 0.298

Gnomad4 ASJ exome AF: 0.366

Gnomad4 EAS exome AF: 0.513

Gnomad4 SAS exome AF: 0.262

Gnomad4 FIN exome AF: 0.370

Gnomad4 NFE exome AF: 0.341

Gnomad4 OTH exome AF: 0.352

GnomAD4 genome AF: 0.336 AC: 49771 AN: 148054 Hom.: 8272 Cov.: 31 AF XY: 0.335 AC XY: 24206 AN XY: 72180

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.323

Alfa AF: 0.329 Hom.: 1846

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
Dann	Benign	0.80

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

LitVar

Other links and lift over

dbSNP: rs2290279; hg19: chr18-10526187; COSMIC: COSV59798257; COSMIC: COSV59798257;