11-114519384-C-T

Position:

• chr11-114519384-C-T

Variant summary

Our verdict is Benign. Variant got -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

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:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NXPE1	NM_001395504.1	c.*2584G>A		3_prime_UTR_variant	9/9	ENST00000534921.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NXPE1	ENST00000534921.3	c.*2584G>A		3_prime_UTR_variant	9/9	3	NM_001395504.1	P1
NXPE1	ENST00000696071.1	c.*2584G>A		3_prime_UTR_variant	8/8			P1

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

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.218

Alfa AF: 0.190 Hom.: 496

Bravo AF: 0.246

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9326244; hg19: chr11-114390106;