7-8702851-C-T

Variant names:

• chr7-8702851-C-T
• rs10253965
• NM_152745.3:c.55-48157C>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.55-48157C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,826 control chromosomes in the GnomAD database, including 19,307 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 0.49 (19307 hom., cov: 31)
• Consequence: NXPH1 NM_152745.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXPH1	NM_152745.3	c.55-48157C>T		intron_variant	Intron 2 of 2	ENST00000405863.6	NP_689958.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NXPH1	ENST00000405863.6	c.55-48157C>T		intron_variant	Intron 2 of 2	1	NM_152745.3	ENSP00000384551.1
NXPH1	ENST00000429542.1	c.55-48157C>T		intron_variant	Intron 1 of 1	1		ENSP00000408216.1
NXPH1	ENST00000438764.1	c.55-48157C>T		intron_variant	Intron 2 of 2	4		ENSP00000404689.1
NXPH1	ENST00000497400.1	n.59+12506C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74598 AN: 151708 Hom.: 19274 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.492 AC: 74666 AN: 151826 Hom.: 19307 Cov.: 31 AF XY: 0.493 AC XY: 36564 AN XY: 74210

African (AFR) AF: 0.632 AC: 26133 AN: 41376

American (AMR) AF: 0.469 AC: 7148 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3468

East Asian (EAS) AF: 0.796 AC: 4108 AN: 5160

South Asian (SAS) AF: 0.426 AC: 2053 AN: 4816

European-Finnish (FIN) AF: 0.440 AC: 4640 AN: 10554

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27885 AN: 67916

Other (OTH) AF: 0.466 AC: 980 AN: 2102

Alfa AF: 0.425 Hom.: 8563

Bravo AF: 0.504

Asia WGS AF: 0.592 AC: 2060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.62
PhyloP100		-0.047
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: rs10253965; hg19: chr7-8742481;