rs2349775

Variant names:

• chr7-8678450-G-A
• rs2349775
• NM_152745.3:c.55-72558G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-8678450-G-A
• chr7-8678450-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.55-72558G>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
• Publications: 17 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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.55-72558G>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.55-72558G>A		intron	N/A	ENSP00000384551.1
	NXPH1	ENST00000429542.1	TSL:1	c.55-72558G>A		intron	N/A	ENSP00000408216.1
	NXPH1	ENST00000438764.1	TSL:4	c.55-72558G>A		intron	N/A	ENSP00000404689.1

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

African (AFR) AF: 0.914 AC: 37945 AN: 41534

American (AMR) AF: 0.842 AC: 12879 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2718 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5178 AN: 5184

South Asian (SAS) AF: 0.876 AC: 4220 AN: 4816

European-Finnish (FIN) AF: 0.712 AC: 7528 AN: 10566

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.729 AC: 49537 AN: 67978

Other (OTH) AF: 0.812 AC: 1717 AN: 2114

Alfa AF: 0.765 Hom.: 116104

Bravo AF: 0.819

Asia WGS AF: 0.943 AC: 3278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.32
PhyloP100		-0.54
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: rs2349775; hg19: chr7-8718080;