rs510110

Variant names:

• chr18-10540435-A-C
• rs510110
• NM_003826.3:c.506+36A>C

Your query was ambiguous. Multiple possible variants found:

• chr18-10540435-A-C
• chr18-10540435-A-G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607
• Publications: 5 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAPG	NM_003826.3	c.506+36A>C		intron_variant	Intron 8 of 11	ENST00000322897.11	NP_003817.1
NAPG	XM_011525754.3	c.686+36A>C		intron_variant	Intron 9 of 12		XP_011524056.1
NAPG	XM_011525756.3	c.260+36A>C		intron_variant	Intron 6 of 9		XP_011524058.1
NAPG	XM_017026063.3	c.251+36A>C		intron_variant	Intron 4 of 7		XP_016881552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAPG	ENST00000322897.11	c.506+36A>C		intron_variant	Intron 8 of 11	1	NM_003826.3	ENSP00000324628.6

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52270 AN: 151998 Hom.: 9044 Cov.: 33

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

GnomAD2 exomes AF: 0.341 AC: 80687 AN: 236844 AF XY: 0.340

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 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.: 22 AF XY: 0.344 AC XY: 241518 AN XY: 701846

African (AFR) AF: 0.345 AC: 11069 AN: 32052

American (AMR) AF: 0.296 AC: 12622 AN: 42570

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 8775 AN: 25422

East Asian (EAS) AF: 0.449 AC: 17699 AN: 39406

South Asian (SAS) AF: 0.292 AC: 24191 AN: 82972

European-Finnish (FIN) AF: 0.324 AC: 16602 AN: 51174

Middle Eastern (MID) AF: 0.355 AC: 1996 AN: 5618

European-Non Finnish (NFE) AF: 0.349 AC: 373239 AN: 1068524

Other (OTH) AF: 0.339 AC: 19876 AN: 58558

GnomAD4 genome AF: 0.344 AC: 52287 AN: 152116 Hom.: 9049 Cov.: 33 AF XY: 0.342 AC XY: 25403 AN XY: 74336

African (AFR) AF: 0.344 AC: 14276 AN: 41486

American (AMR) AF: 0.322 AC: 4917 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1138 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2137 AN: 5182

South Asian (SAS) AF: 0.294 AC: 1418 AN: 4826

European-Finnish (FIN) AF: 0.322 AC: 3405 AN: 10570

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23781 AN: 67974

Other (OTH) AF: 0.349 AC: 738 AN: 2114

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
PhyloP100		-0.61
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs510110; hg19: chr18-10540432; COSMIC: COSV59796628; COSMIC: COSV59796628;