7-8711802-C-T

Variant names:

• chr7-8711802-C-T
• rs1017002
• NM_152745.3:c.55-39206C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152745.3(NXPH1):​c.55-39206C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,076 control chromosomes in the GnomAD database, including 37,018 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 0.69 (37018 hom., cov: 31)
• Consequence: NXPH1 NM_152745.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXPH1	NM_152745.3	c.55-39206C>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.55-39206C>T		intron_variant	Intron 2 of 2	1	NM_152745.3	ENSP00000384551.1
NXPH1	ENST00000429542.1	c.55-39206C>T		intron_variant	Intron 1 of 1	1		ENSP00000408216.1
NXPH1	ENST00000438764.1	c.55-39206C>T		intron_variant	Intron 2 of 2	4		ENSP00000404689.1
NXPH1	ENST00000497400.1	n.59+21457C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104870 AN: 151958 Hom.: 36968 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.690 AC: 104981 AN: 152076 Hom.: 37018 Cov.: 31 AF XY: 0.695 AC XY: 51649 AN XY: 74340

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.691

Alfa AF: 0.617 Hom.: 40932

Bravo AF: 0.694

Asia WGS AF: 0.727 AC: 2532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.34

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: rs1017002; hg19: chr7-8751432;