NM_003826.3:c.795+269C>T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003826.3(NAPG):​c.795+269C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAPG	NM_003826.3	c.795+269C>T		intron_variant	Intron 11 of 11	ENST00000322897.11	NP_003817.1
NAPG	XM_011525754.3	c.975+269C>T		intron_variant	Intron 12 of 12		XP_011524056.1
NAPG	XM_011525756.3	c.549+269C>T		intron_variant	Intron 9 of 9		XP_011524058.1
NAPG	XM_017026063.3	c.540+269C>T		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>T		intron_variant	Intron 11 of 11	1	NM_003826.3	ENSP00000324628.6
NAPG	ENST00000580224.5	n.*658+269C>T		intron_variant	Intron 10 of 10	2		ENSP00000463265.1
NAPG	ENST00000580483.5	n.*536+269C>T		intron_variant	Intron 7 of 7	3		ENSP00000464496.1
NAPG	ENST00000583367.1	n.1175+269C>T		intron_variant	Intron 6 of 6	2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.060
DANN	Benign	0.88
PhyloP100		-0.20

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: rs617040; hg19: chr18-10549362;