rs9326244

Variant names:

• chr11-114519384-C-T
• rs9326244
• NM_001395504.1:c.*2584G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395504.1(NXPE1):​c.*2584G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,040 control chromosomes in the GnomAD database, including 5,665 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 0.23 (5665 hom., cov: 32)
• Consequence: NXPE1 NM_001395504.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 6 publications found

Genes affected

NXPE1 (HGNC:28527): (neurexophilin and PC-esterase domain family member 1) Predicted to be located in extracellular region. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

NXPE2 (HGNC:26331): (neurexophilin and PC-esterase domain family member 2) Predicted to be integral component of membrane. [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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395504.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NXPE1	NM_001395504.1	MANE Select	c.*2584G>A		3_prime_UTR	Exon 9 of 9	NP_001382433.1	Q8N323-1
	NXPE1	NM_001367953.1		c.*2584G>A		3_prime_UTR	Exon 8 of 8	NP_001354882.1	Q8N323-1
	NXPE1	NM_152315.5		c.*2584G>A		3_prime_UTR	Exon 6 of 6	NP_689528.2	Q8N323-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NXPE1	ENST00000534921.3	TSL:3 MANE Select	c.*2584G>A		3_prime_UTR	Exon 9 of 9	ENSP00000439503.2	Q8N323-1
	NXPE1	ENST00000696071.1		c.*2584G>A		3_prime_UTR	Exon 8 of 8	ENSP00000512373.1	Q8N323-1
	NXPE1	ENST00000867473.1		c.*2584G>A		3_prime_UTR	Exon 7 of 7	ENSP00000537532.1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34781 AN: 151922 Hom.: 5651 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.229 AC: 34833 AN: 152040 Hom.: 5665 Cov.: 32 AF XY: 0.227 AC XY: 16870 AN XY: 74328

African (AFR) AF: 0.453 AC: 18763 AN: 41424

American (AMR) AF: 0.218 AC: 3320 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3466

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5186

South Asian (SAS) AF: 0.228 AC: 1101 AN: 4824

European-Finnish (FIN) AF: 0.109 AC: 1152 AN: 10570

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9062 AN: 67990

Other (OTH) AF: 0.218 AC: 460 AN: 2110

Alfa AF: 0.277 Hom.: 2832

Bravo AF: 0.246

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.13
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs9326244; hg19: chr11-114390106;