rs1080074

chr11-114556704-T-C

Variant summary

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

The NM_001395504.1(NXPE1):c.-211+3094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,040 control chromosomes in the GnomAD database, including 1,137 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 0.11 (1137 hom., cov: 30)
• Consequence: NXPE1 NM_001395504.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NXPE1	NM_001395504.1	c.-211+3094A>G		intron_variant		ENST00000534921.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NXPE1	ENST00000534921.3	c.-211+3094A>G		intron_variant		3	NM_001395504.1	P1
NXPE1	ENST00000251921.6	c.-357+3094A>G		intron_variant		1
NXPE1	ENST00000696071.1	c.-99+3094A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16780 AN: 151922 Hom.: 1137 Cov.: 30

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0705

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.110 AC: 16780 AN: 152040 Hom.: 1137 Cov.: 30 AF XY: 0.112 AC XY: 8289 AN XY: 74284

Gnomad4 AFR AF: 0.0279

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0706

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.133

Alfa AF: 0.130 Hom.: 629

Bravo AF: 0.107

Asia WGS AF: 0.119 AC: 411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.0
Dann	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs1080074; hg19: chr11-114427426;