rs10496799

Variant names:

• chr2-138670099-T-C
• rs10496799
• NM_007226.3:c.*823A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXPH2	NM_007226.3	c.*823A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000272641.4	NP_009157.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NXPH2	ENST00000272641.4	c.*823A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_007226.3	ENSP00000272641.3

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

African (AFR) AF: 0.327 AC: 13569 AN: 41488

American (AMR) AF: 0.293 AC: 4480 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3472

East Asian (EAS) AF: 0.166 AC: 861 AN: 5184

South Asian (SAS) AF: 0.223 AC: 1076 AN: 4820

European-Finnish (FIN) AF: 0.251 AC: 2661 AN: 10586

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

European-Non Finnish (NFE) AF: 0.312 AC: 21182 AN: 67982

Other (OTH) AF: 0.295 AC: 620 AN: 2104

Alfa AF: 0.300 Hom.: 29841

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10496799; hg19: chr2-139427669;