X-74739491-C-T

Variant summary

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

The NM_001008537.3(NEXMIF):​c.4465G>A​(p.Asp1489Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,074,334 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. D1489D) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 21)
Exomes 𝑓: 0.0000056 ( 0 hom. 2 hem. )

Consequence

NEXMIF
NM_001008537.3 missense

Scores

16

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 0.128
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 -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.03272724).
BS2
High Hemizygotes in GnomAdExome4 at 2 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NEXMIFNM_001008537.3 linkuse as main transcriptc.4465G>A p.Asp1489Asn missense_variant 4/4 ENST00000055682.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NEXMIFENST00000055682.12 linkuse as main transcriptc.4465G>A p.Asp1489Asn missense_variant 4/41 NM_001008537.3 P1
NEXMIFENST00000616200.2 linkuse as main transcriptc.4465G>A p.Asp1489Asn missense_variant 4/51 P1
NEXMIFENST00000642681.2 linkuse as main transcriptc.*605G>A 3_prime_UTR_variant 3/3

Frequencies

GnomAD3 genomes
Cov.:
21
GnomAD3 exomes
AF:
0.0000121
AC:
2
AN:
165637
Hom.:
0
AF XY:
0.0000189
AC XY:
1
AN XY:
52933
show subpopulations
Gnomad AFR exome
AF:
0.00
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:
0.00
Gnomad NFE exome
AF:
0.0000271
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000558
AC:
6
AN:
1074334
Hom.:
0
Cov.:
25
AF XY:
0.00000585
AC XY:
2
AN XY:
341816
show subpopulations
Gnomad4 AFR exome
AF:
0.0000776
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000485
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
21
Bravo
AF:
0.0000113
ExAC
AF:
0.0000247
AC:
3

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Uncertain:2
Uncertain significance, criteria provided, single submitterclinical testingGeneDxJan 28, 2020In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMar 08, 2023In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The asparagine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1313198). This variant has not been reported in the literature in individuals affected with NEXMIF-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 1489 of the NEXMIF protein (p.Asp1489Asn). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.070
BayesDel_addAF
Benign
-0.45
T
BayesDel_noAF
Benign
-0.89
CADD
Benign
5.5
DANN
Benign
0.92
DEOGEN2
Benign
0.057
T;T
FATHMM_MKL
Benign
0.091
N
LIST_S2
Benign
0.65
.;T
M_CAP
Benign
0.016
T
MetaRNN
Benign
0.033
T;T
MetaSVM
Benign
-1.0
T
MutationTaster
Benign
1.0
N;N
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-0.24
N;.
REVEL
Benign
0.019
Sift
Benign
0.23
T;.
Sift4G
Benign
0.65
T;T
Polyphen
0.013
B;B
Vest4
0.14
MutPred
0.23
Loss of stability (P = 0.0951);Loss of stability (P = 0.0951);
MVP
0.16
MPC
0.22
ClinPred
0.035
T
GERP RS
0.63
Varity_R
0.058
gMVP
0.31

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
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: rs751841142; hg19: chrX-73959326; API