rs11681160

Variant names:

• chr2-138752702-G-A
• rs11681160
• NM_007226.3:c.51+27489C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007226.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NXPH2	NM_007226.3	MANE Select	c.51+27489C>T		intron	N/A	NP_009157.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NXPH2	ENST00000272641.4	TSL:1 MANE Select	c.51+27489C>T		intron	N/A	ENSP00000272641.3

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

African (AFR) AF: 0.217 AC: 8979 AN: 41422

American (AMR) AF: 0.198 AC: 3025 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3472

East Asian (EAS) AF: 0.00387 AC: 20 AN: 5170

South Asian (SAS) AF: 0.180 AC: 868 AN: 4820

European-Finnish (FIN) AF: 0.404 AC: 4253 AN: 10528

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23887 AN: 67950

Other (OTH) AF: 0.259 AC: 546 AN: 2108

Alfa AF: 0.313 Hom.: 13287

Bravo AF: 0.259

Asia WGS AF: 0.0870 AC: 303 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.088
DANN	Benign	0.79
PhyloP100		-1.5
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: rs11681160; hg19: chr2-139510272;