7-8596922-C-T

Variant names:

• chr7-8596922-C-T
• rs2107281
• NM_152745.3:c.55-154086C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152745.3(NXPH1):​c.55-154086C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0898 in 152,010 control chromosomes in the GnomAD database, including 1,445 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 0.090 (1445 hom., cov: 32)
• Consequence: NXPH1 NM_152745.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 2 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]

LOC105375144 (HGNC:):

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 = 0.228 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NXPH1	NM_152745.3	MANE Select	c.55-154086C>T		intron	N/A	NP_689958.1	P58417

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NXPH1	ENST00000405863.6	TSL:1 MANE Select	c.55-154086C>T		intron	N/A	ENSP00000384551.1	P58417
	NXPH1	ENST00000429542.1	TSL:1	c.55-154086C>T		intron	N/A	ENSP00000408216.1	C9JPD0
	NXPH1	ENST00000438764.1	TSL:4	c.55-154086C>T		intron	N/A	ENSP00000404689.1	C9JE46

Frequencies

GnomAD3 genomes AF: 0.0897 AC: 13622 AN: 151892 Hom.: 1434 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.00736

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0131

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0898 AC: 13649 AN: 152010 Hom.: 1445 Cov.: 32 AF XY: 0.0932 AC XY: 6927 AN XY: 74322

African (AFR) AF: 0.232 AC: 9623 AN: 41422

American (AMR) AF: 0.0426 AC: 650 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3466

East Asian (EAS) AF: 0.238 AC: 1227 AN: 5158

South Asian (SAS) AF: 0.180 AC: 871 AN: 4826

European-Finnish (FIN) AF: 0.00736 AC: 78 AN: 10592

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0131 AC: 891 AN: 67970

Other (OTH) AF: 0.0805 AC: 170 AN: 2112

Alfa AF: 0.0307 Hom.: 195

Bravo AF: 0.0968

Asia WGS AF: 0.238 AC: 827 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	0.81
DANN	Benign	0.53
PhyloP100		-0.40
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: rs2107281; hg19: chr7-8636552;