X-74739447-A-G

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001008537.3(NEXMIF):ā€‹c.4509T>Cā€‹(p.Pro1503=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00105 in 1,198,042 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 372 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.00052 ( 0 hom., 10 hem., cov: 21)
Exomes š‘“: 0.0011 ( 0 hom. 362 hem. )

Consequence

NEXMIF
NM_001008537.3 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 6.42
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant X-74739447-A-G is Benign according to our data. Variant chrX-74739447-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 211270.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Hemizygotes in GnomAd4 at 10 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NEXMIFNM_001008537.3 linkuse as main transcriptc.4509T>C p.Pro1503= synonymous_variant 4/4 ENST00000055682.12 NP_001008537.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NEXMIFENST00000055682.12 linkuse as main transcriptc.4509T>C p.Pro1503= synonymous_variant 4/41 NM_001008537.3 ENSP00000055682 P1
NEXMIFENST00000616200.2 linkuse as main transcriptc.4509T>C p.Pro1503= synonymous_variant 4/51 ENSP00000480284 P1
NEXMIFENST00000642681.2 linkuse as main transcriptc.*649T>C 3_prime_UTR_variant 3/3 ENSP00000495800

Frequencies

GnomAD3 genomes
AF:
0.000516
AC:
57
AN:
110384
Hom.:
0
Cov.:
21
AF XY:
0.000307
AC XY:
10
AN XY:
32590
show subpopulations
Gnomad AFR
AF:
0.000198
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000984
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000946
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000614
AC:
102
AN:
166139
Hom.:
0
AF XY:
0.000681
AC XY:
37
AN XY:
54297
show subpopulations
Gnomad AFR exome
AF:
0.000321
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000127
Gnomad NFE exome
AF:
0.00124
Gnomad OTH exome
AF:
0.000485
GnomAD4 exome
AF:
0.00110
AC:
1200
AN:
1087605
Hom.:
0
Cov.:
27
AF XY:
0.00102
AC XY:
362
AN XY:
354997
show subpopulations
Gnomad4 AFR exome
AF:
0.0000772
Gnomad4 AMR exome
AF:
0.0000609
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000124
Gnomad4 NFE exome
AF:
0.00139
Gnomad4 OTH exome
AF:
0.000591
GnomAD4 genome
AF:
0.000516
AC:
57
AN:
110437
Hom.:
0
Cov.:
21
AF XY:
0.000306
AC XY:
10
AN XY:
32653
show subpopulations
Gnomad4 AFR
AF:
0.000197
Gnomad4 AMR
AF:
0.0000982
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000946
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.00102
Hom.:
8
Bravo
AF:
0.000578

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 25, 2024- -
Benign, criteria provided, single submitterclinical testingGeneDxSep 25, 2019- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2024NEXMIF: BP4, BS2 -
not specified Benign:2
Likely benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoDec 17, 2015- -
Benign, criteria provided, single submitterclinical testingAmbry GeneticsOct 20, 2017This 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. -
NEXMIF-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesSep 10, 2019This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
8.1
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

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

Other links and lift over

dbSNP: rs41303725; hg19: chrX-73959282; API