Variant rs79916924 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_001395504.1(NXPE1):c.1640G>T(p.Cys547Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0006 in 1,607,022 control chromosomes in the GnomAD database, including 5 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 0.00098 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00056 ( 5 hom. )

Consequence

NXPE1
NM_001395504.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.99

Variant links:

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]

NXPE1 links:

NXPE2 (HGNC:):

NXPE2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.014774412).

BS2

High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NXPE1	NM_001395504.1 linkuse as main transcript	c.1640G>T	p.Cys547Phe	missense_variant	9/9	ENST00000534921.3	NP_001382433.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NXPE1	ENST00000534921.3 linkuse as main transcript	c.1640G>T	p.Cys547Phe	missense_variant	9/9	3	NM_001395504.1	ENSP00000439503	P1	Q8N323-1
NXPE1	ENST00000251921.6 linkuse as main transcript	c.1214G>T	p.Cys405Phe	missense_variant	6/6	1		ENSP00000251921		Q8N323-2
NXPE1	ENST00000536271.5 linkuse as main transcript	n.2032G>T		non_coding_transcript_exon_variant	4/4	1
NXPE1	ENST00000696071.1 linkuse as main transcript	c.1640G>T	p.Cys547Phe	missense_variant	8/8			ENSP00000512373	P1	Q8N323-1

Frequencies

GnomAD3 genomes

AF:

0.000979

AC:

149

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00944

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000500

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.00116

AC:

289

AN:

248564

Hom.:

AF XY:

0.00127

AC XY:

170

AN XY:

134226

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000873

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00180

Gnomad SAS exome

AF:

0.000700

Gnomad FIN exome

AF:

0.00740

Gnomad NFE exome

AF:

0.000605

Gnomad OTH exome

AF:

0.000993

GnomAD4 exome

AF:

0.000560

AC:

815

AN:

1454742

Hom.:

Cov.:

AF XY:

0.000608

AC XY:

440

AN XY:

723282

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000899

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00245

Gnomad4 SAS exome

AF:

0.00116

Gnomad4 FIN exome

AF:

0.00648

Gnomad4 NFE exome

AF:

0.000203

Gnomad4 OTH exome

AF:

0.000732

GnomAD4 genome

AF:

0.000978

AC:

149

AN:

152280

Hom.:

Cov.:

AF XY:

0.00137

AC XY:

102

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.0000241

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00193

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00944

Gnomad4 NFE

AF:

0.000500

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.000507

Hom.:

Bravo

AF:

0.000272

ExAC

AF:

0.00110

AC:

133

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.000109

EpiControl

AF:

0.000297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.56

BayesDel_addAF

Benign

-0.083

BayesDel_noAF

Uncertain

0.10

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.26

T;.;T

Eigen

Pathogenic

0.79

Eigen_PC

Pathogenic

0.70

FATHMM_MKL

Uncertain

0.95

LIST_S2

Uncertain

0.90

.;D;D

M_CAP

Benign

0.036

MetaRNN

Benign

0.015

T;T;T

MetaSVM

Benign

-0.52

MutationAssessor

Pathogenic

3.8

H;.;H

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.55

PROVEAN

Pathogenic

-9.9

.;D;D

REVEL

Uncertain

0.47

Sift

Pathogenic

0.0

.;D;D

Sift4G

Pathogenic

0.0

.;D;D

Polyphen

1.0

D;.;D

Vest4

0.81, 0.81

MVP

0.22

MPC

0.19

ClinPred

0.22

GERP RS

4.6

Varity_R

0.92

gMVP

0.35

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over