chrX-74740311-G-A

Position:

chrX-74740311-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001008537.3(NEXMIF):c.4246C>T(p.Pro1416Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00363 in 1,209,131 control chromosomes in the GnomAD database, including 11 homozygotes. There are 1,713 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0030 ( 0 hom., 94 hem., cov: 22)

Exomes 𝑓: 0.0037 ( 11 hom. 1619 hem. )

Consequence

NEXMIF
NM_001008537.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 2.79

Variant links:

Genes affected

NEXMIF (HGNC:29433): (neurite extension and migration factor) An inversion on the X chromosome which disrupts this gene and a G-protein coupled purinergic receptor gene located in the pseudoautosomal region of the X chromosome has been linked to X linked cognitive disability.[provided by RefSeq, Mar 2009]

NEXMIF links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005046755).

BP6

Variant X-74740311-G-A is Benign according to our data. Variant chrX-74740311-G-A is described in ClinVar as [Benign]. Clinvar id is 211269.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-74740311-G-A is described in Lovd as [Likely_benign]. Variant chrX-74740311-G-A is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00369 (4054/1097738) while in subpopulation MID AF= 0.021 (87/4135). AF 95% confidence interval is 0.0179. There are 11 homozygotes in gnomad4_exome. There are 1619 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd4 at 94 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEXMIF	NM_001008537.3 linkuse as main transcript	c.4246C>T	p.Pro1416Ser	missense_variant	3/4	ENST00000055682.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
NEXMIF	ENST00000055682.12 linkuse as main transcript	c.4246C>T	p.Pro1416Ser	missense_variant	3/4	1	NM_001008537.3	P1
NEXMIF	ENST00000616200.2 linkuse as main transcript	c.4246C>T	p.Pro1416Ser	missense_variant	3/5	1		P1
NEXMIF	ENST00000642681.2 linkuse as main transcript	c.4246C>T	p.Pro1416Ser	missense_variant	3/3

Frequencies

GnomAD3 genomes

AF:

0.00297

AC:

331

AN:

111339

Hom.:

Cov.:

AF XY:

0.00283

AC XY:

AN XY:

33561

show subpopulations

Gnomad AFR

AF:

0.000458

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00210

Gnomad ASJ

AF:

0.00189

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0191

Gnomad FIN

AF:

0.000999

Gnomad MID

AF:

0.0169

Gnomad NFE

AF:

0.00420

Gnomad OTH

AF:

0.00469

GnomAD3 exomes

AF:

0.00422

AC:

772

AN:

183046

Hom.:

AF XY:

0.00555

AC XY:

375

AN XY:

67622

show subpopulations

Gnomad AFR exome

AF:

0.000152

Gnomad AMR exome

AF:

0.00310

Gnomad ASJ exome

AF:

0.00375

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0179

Gnomad FIN exome

AF:

0.000627

Gnomad NFE exome

AF:

0.00359

Gnomad OTH exome

AF:

0.00266

GnomAD4 exome

AF:

0.00369

AC:

4054

AN:

1097738

Hom.:

Cov.:

AF XY:

0.00446

AC XY:

1619

AN XY:

363126

show subpopulations

Gnomad4 AFR exome

AF:

0.000379

Gnomad4 AMR exome

AF:

0.00298

Gnomad4 ASJ exome

AF:

0.00356

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0189

Gnomad4 FIN exome

AF:

0.000568

Gnomad4 NFE exome

AF:

0.00301

Gnomad4 OTH exome

AF:

0.00449

GnomAD4 genome

AF:

0.00296

AC:

330

AN:

111393

Hom.:

Cov.:

AF XY:

0.00280

AC XY:

AN XY:

33625

show subpopulations

Gnomad4 AFR

AF:

0.000457

Gnomad4 AMR

AF:

0.00210

Gnomad4 ASJ

AF:

0.00189

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0187

Gnomad4 FIN

AF:

0.000999

Gnomad4 NFE

AF:

0.00420

Gnomad4 OTH

AF:

0.00463

Alfa

AF:

0.00364

Hom.:

162

Bravo

AF:

0.00232

TwinsUK

AF:

0.00324

AC:

ALSPAC

AF:

0.00346

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00386

AC:

ExAC

AF:

0.00459

AC:

557

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:6

Likely benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 29, 2024	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jan 24, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Apr 01, 2016	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 17, 2019	- -

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Aug 04, 2017	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Jun 24, 2016	This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.72

CADD

Benign

DANN

Benign

0.79

DEOGEN2

Benign

0.026

T;T;.

FATHMM_MKL

Benign

0.64

LIST_S2

Benign

0.63

.;T;T

MetaRNN

Benign

0.0050

T;T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.26

N;.;.

REVEL

Benign

0.043

Sift

Benign

0.16

T;.;.

Sift4G

Benign

0.54

T;T;.

Polyphen

0.0030

B;B;.

Vest4

0.043

MVP

0.11

MPC

0.23

ClinPred

0.0017

GERP RS

0.95

Varity_R

0.033

gMVP

0.054

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over