7-8454756-A-G

Position:

• chr7-8454756-A-G

Variant summary

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

The NM_152745.3(NXPH1):​c.54+18989A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,990 control chromosomes in the GnomAD database, including 20,209 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 0.51 (20209 hom., cov: 32)
• Consequence: NXPH1 NM_152745.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NXPH1	NM_152745.3	c.54+18989A>G		intron_variant		ENST00000405863.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NXPH1	ENST00000405863.6	c.54+18989A>G		intron_variant		1	NM_152745.3	P1
NXPH1	ENST00000429542.1	c.54+18989A>G		intron_variant		1
NXPH1	ENST00000438764.1	c.54+18989A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77220 AN: 151872 Hom.: 20198 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.508 AC: 77272 AN: 151990 Hom.: 20209 Cov.: 32 AF XY: 0.510 AC XY: 37883 AN XY: 74324

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.481

Alfa AF: 0.472 Hom.: 12535

Bravo AF: 0.518

Asia WGS AF: 0.673 AC: 2339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.43
DANN	Benign	0.51

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: rs1476623; hg19: chr7-8494386;