rs2349775

Positions:

• chr7-8678450-G-A
• chr7-8678450-G-C

Variant summary

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

The NM_152745.3(NXPH1):​c.55-72558G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,160 control chromosomes in the GnomAD database, including 50,093 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 0.81 (50093 hom., cov: 31)
• Consequence: NXPH1 NM_152745.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542

Genes affected

NXPH1 (HGNC:20693): (neurexophilin 1) This gene is a member of the neurexophilin family and encodes a secreted protein with a variable N-terminal domain, a highly conserved, N-glycosylated central domain, a short linker region, and a cysteine-rich C-terminal domain. This protein forms a very tight complex with alpha neurexins, a group of proteins that promote adhesion between dendrites and axons. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NXPH1	NM_152745.3	c.55-72558G>A		intron_variant		ENST00000405863.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NXPH1	ENST00000405863.6	c.55-72558G>A		intron_variant		1	NM_152745.3	P1
NXPH1	ENST00000429542.1	c.55-72558G>A		intron_variant		1
NXPH1	ENST00000438764.1	c.55-72558G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122503 AN: 152042 Hom.: 50027 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.806 AC: 122626 AN: 152160 Hom.: 50093 Cov.: 31 AF XY: 0.810 AC XY: 60219 AN XY: 74384

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.812

Alfa AF: 0.752 Hom.: 61320

Bravo AF: 0.819

Asia WGS AF: 0.943 AC: 3278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.32

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

LitVar

Other links and lift over

dbSNP: rs2349775; hg19: chr7-8718080;