rs1013812

Variant names:

• chr7-8683058-G-A
• rs1013812
• NM_152745.3:c.55-67950G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-8683058-G-A
• chr7-8683058-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152745.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NXPH1	NM_152745.3	MANE Select	c.55-67950G>A		intron	N/A	NP_689958.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NXPH1	ENST00000405863.6	TSL:1 MANE Select	c.55-67950G>A		intron	N/A	ENSP00000384551.1
	NXPH1	ENST00000429542.1	TSL:1	c.55-67950G>A		intron	N/A	ENSP00000408216.1
	NXPH1	ENST00000438764.1	TSL:4	c.55-67950G>A		intron	N/A	ENSP00000404689.1

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

African (AFR) AF: 0.417 AC: 17284 AN: 41468

American (AMR) AF: 0.381 AC: 5821 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3468

East Asian (EAS) AF: 0.623 AC: 3212 AN: 5152

South Asian (SAS) AF: 0.314 AC: 1513 AN: 4822

European-Finnish (FIN) AF: 0.358 AC: 3782 AN: 10562

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21441 AN: 67978

Other (OTH) AF: 0.341 AC: 719 AN: 2110

Alfa AF: 0.330 Hom.: 25697

Bravo AF: 0.372

Asia WGS AF: 0.462 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.69
PhyloP100		0.60
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: rs1013812; hg19: chr7-8722688;