rs11681160

chr2-138752702-G-A

Variant summary

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

The NM_007226.3(NXPH2):c.51+27489C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,930 control chromosomes in the GnomAD database, including 6,657 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 0.28 (6657 hom., cov: 32)
• Consequence: NXPH2 NM_007226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

NXPH2 (HGNC:8076): (neurexophilin 2) Predicted to enable signaling receptor binding activity. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NXPH2	NM_007226.3	c.51+27489C>T		intron_variant		ENST00000272641.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NXPH2	ENST00000272641.4	c.51+27489C>T		intron_variant		1	NM_007226.3	P1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42420 AN: 151812 Hom.: 6656 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.279 AC: 42424 AN: 151930 Hom.: 6657 Cov.: 32 AF XY: 0.276 AC XY: 20462 AN XY: 74242

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.00387

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.259

Alfa AF: 0.318 Hom.: 10727

Bravo AF: 0.259

Asia WGS AF: 0.0870 AC: 303 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.088
Dann	Benign	0.79

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: rs11681160; hg19: chr2-139510272;