rs10496799

chr2-138670099-T-C

Variant summary

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

The NM_007226.3(NXPH2):c.*823A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,124 control chromosomes in the GnomAD database, including 6,960 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 0.30 (6960 hom., cov: 33)
• Consequence: NXPH2 NM_007226.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

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 (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NXPH2	NM_007226.3	c.*823A>G		3_prime_UTR_variant	2/2	ENST00000272641.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NXPH2	ENST00000272641.4	c.*823A>G		3_prime_UTR_variant	2/2	1	NM_007226.3	P1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45424 AN: 152006 Hom.: 6952 Cov.: 33

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.299 AC: 45461 AN: 152124 Hom.: 6960 Cov.: 33 AF XY: 0.294 AC XY: 21840 AN XY: 74366

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.295

Alfa AF: 0.299 Hom.: 14029

Bravo AF: 0.304

Asia WGS AF: 0.211 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.032
Dann	Benign	0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10496799; hg19: chr2-139427669;