X-5892715-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_181332.3(NLGN4X):c.*102G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 1,112,611 control chromosomes in the GnomAD database, including 41,117 homozygotes. There are 106,097 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.38 ( 6558 hom., 11781 hem., cov: 22)
Exomes 𝑓: 0.31 ( 34559 hom. 94316 hem. )
Consequence
NLGN4X
NM_181332.3 3_prime_UTR
NM_181332.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.452
Publications
8 publications found
Genes affected
NLGN4X (HGNC:14287): (neuroligin 4 X-linked) This gene encodes a member of the type-B carboxylesterase/lipase protein family. The encoded protein belongs to a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. The encoded protein interacts with discs large homolog 4 (DLG4). Mutations in this gene have been associated with autism and Asperger syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
NLGN4X Gene-Disease associations (from GenCC):
- X-linked complex neurodevelopmental disorderInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
- autism, susceptibility to, X-linked 2Inheritance: XL Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
Variant X-5892715-C-T is Benign according to our data. Variant chrX-5892715-C-T is described in ClinVar as [Benign]. Clinvar id is 1238862.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLGN4X | NM_181332.3 | c.*102G>A | 3_prime_UTR_variant | Exon 6 of 6 | ENST00000381095.8 | NP_851849.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.378 AC: 41590AN: 110091Hom.: 6558 Cov.: 22 show subpopulations
GnomAD3 genomes
AF:
AC:
41590
AN:
110091
Hom.:
Cov.:
22
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.308 AC: 309113AN: 1002466Hom.: 34559 Cov.: 19 AF XY: 0.311 AC XY: 94316AN XY: 302982 show subpopulations
GnomAD4 exome
AF:
AC:
309113
AN:
1002466
Hom.:
Cov.:
19
AF XY:
AC XY:
94316
AN XY:
302982
show subpopulations
African (AFR)
AF:
AC:
14991
AN:
24338
American (AMR)
AF:
AC:
8208
AN:
29331
Ashkenazi Jewish (ASJ)
AF:
AC:
5557
AN:
17954
East Asian (EAS)
AF:
AC:
4084
AN:
28201
South Asian (SAS)
AF:
AC:
12532
AN:
48041
European-Finnish (FIN)
AF:
AC:
9409
AN:
34089
Middle Eastern (MID)
AF:
AC:
928
AN:
3903
European-Non Finnish (NFE)
AF:
AC:
240220
AN:
773743
Other (OTH)
AF:
AC:
13184
AN:
42866
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
7528
15056
22583
30111
37639
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.378 AC: 41630AN: 110145Hom.: 6558 Cov.: 22 AF XY: 0.363 AC XY: 11781AN XY: 32451 show subpopulations
GnomAD4 genome
AF:
AC:
41630
AN:
110145
Hom.:
Cov.:
22
AF XY:
AC XY:
11781
AN XY:
32451
show subpopulations
African (AFR)
AF:
AC:
18177
AN:
30079
American (AMR)
AF:
AC:
3280
AN:
10384
Ashkenazi Jewish (ASJ)
AF:
AC:
806
AN:
2627
East Asian (EAS)
AF:
AC:
497
AN:
3481
South Asian (SAS)
AF:
AC:
633
AN:
2576
European-Finnish (FIN)
AF:
AC:
1506
AN:
5880
Middle Eastern (MID)
AF:
AC:
44
AN:
216
European-Non Finnish (NFE)
AF:
AC:
15918
AN:
52738
Other (OTH)
AF:
AC:
505
AN:
1490
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
861
1722
2582
3443
4304
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Jun 19, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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