rs10245124

chr7-8602724-T-C

Variant summary

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

The NM_152745.3(NXPH1):c.55-148284T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 152,284 control chromosomes in the GnomAD database, including 350 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 0.051 (350 hom., cov: 32)
• Consequence: NXPH1 NM_152745.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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

Verdict is Benign. Variant got -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 = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NXPH1	NM_152745.3	c.55-148284T>C		intron_variant		ENST00000405863.6
LOC105375144	XR_001745084.2	n.189-8289A>G		intron_variant, non_coding_transcript_variant
LOC105375144	XR_007060208.1	n.182-8289A>G		intron_variant, non_coding_transcript_variant
LOC105375144	XR_927017.4	n.189-8289A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NXPH1	ENST00000405863.6	c.55-148284T>C		intron_variant		1	NM_152745.3	P1
NXPH1	ENST00000429542.1	c.55-148284T>C		intron_variant		1
NXPH1	ENST00000438764.1	c.55-148284T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0506 AC: 7704 AN: 152166 Hom.: 348 Cov.: 32

Gnomad AFR AF: 0.0524

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0278

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0507 AC: 7716 AN: 152284 Hom.: 350 Cov.: 32 AF XY: 0.0533 AC XY: 3973 AN XY: 74478

Gnomad4 AFR AF: 0.0528

Gnomad4 AMR AF: 0.0941

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0567

Gnomad4 NFE AF: 0.0277

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0340 Hom.: 228

Bravo AF: 0.0551

Asia WGS AF: 0.156 AC: 544 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	0.82
Dann	Benign	0.72

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: rs10245124; hg19: chr7-8642354;