chr7-8602724-T-C

Variant names:

• chr7-8602724-T-C
• rs10245124
• NM_152745.3:c.55-148284T>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.55-148284T>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
• 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=-0.89).
• 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 rank	MANE	Protein	UniProt
NXPH1	NM_152745.3	c.55-148284T>C		intron_variant	Intron 2 of 2	ENST00000405863.6	NP_689958.1
LOC105375144	XR_001745084.2	n.189-8289A>G		intron_variant	Intron 2 of 3
LOC105375144	XR_007060208.1	n.182-8289A>G		intron_variant	Intron 2 of 3
LOC105375144	XR_927017.4	n.189-8289A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NXPH1	ENST00000405863.6	c.55-148284T>C		intron_variant	Intron 2 of 2	1	NM_152745.3	ENSP00000384551.1
NXPH1	ENST00000429542.1	c.55-148284T>C		intron_variant	Intron 1 of 1	1		ENSP00000408216.1
NXPH1	ENST00000438764.1	c.55-148284T>C		intron_variant	Intron 2 of 2	4		ENSP00000404689.1

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

African (AFR) AF: 0.0528 AC: 2193 AN: 41566

American (AMR) AF: 0.0941 AC: 1438 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0248 AC: 86 AN: 3468

East Asian (EAS) AF: 0.173 AC: 899 AN: 5186

South Asian (SAS) AF: 0.102 AC: 490 AN: 4824

European-Finnish (FIN) AF: 0.0567 AC: 603 AN: 10626

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0277 AC: 1887 AN: 68008

Other (OTH) AF: 0.0426 AC: 90 AN: 2114

Alfa AF: 0.0381 Hom.: 690

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
PhyloP100		-1.2
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: rs10245124; hg19: chr7-8642354;