rs1013812

chr7-8683058-G-Achr7-8683058-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.55-67950G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,050 control chromosomes in the GnomAD database, including 10,317 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 0.36 (10317 hom., cov: 33)
• Consequence: NXPH1 NM_152745.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NXPH1	NM_152745.3	c.55-67950G>A		intron_variant		ENST00000405863.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NXPH1	ENST00000405863.6	c.55-67950G>A		intron_variant		1	NM_152745.3	P1
NXPH1	ENST00000429542.1	c.55-67950G>A		intron_variant		1
NXPH1	ENST00000438764.1	c.55-67950G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55016 AN: 151932 Hom.: 10305 Cov.: 33

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.362 AC: 55047 AN: 152050 Hom.: 10317 Cov.: 33 AF XY: 0.364 AC XY: 27093 AN XY: 74332

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.341

Alfa AF: 0.320 Hom.: 10462

Bravo AF: 0.372

Asia WGS AF: 0.462 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.69

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: rs1013812; hg19: chr7-8722688;