chrX-5892908-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_181332.3(NLGN4X):c.2360C>T(p.Thr787Met) variant causes a missense change. The variant allele was found at a frequency of 0.000241 in 1,209,295 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 99 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T787T) has been classified as Uncertain significance.
Frequency
Consequence
NM_181332.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLGN4X | NM_181332.3 | c.2360C>T | p.Thr787Met | missense_variant | 6/6 | ENST00000381095.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLGN4X | ENST00000381095.8 | c.2360C>T | p.Thr787Met | missense_variant | 6/6 | 1 | NM_181332.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000162 AC: 18AN: 111005Hom.: 0 Cov.: 22 AF XY: 0.000211 AC XY: 7AN XY: 33211
GnomAD3 exomes AF: 0.000218 AC: 40AN: 183527Hom.: 0 AF XY: 0.000250 AC XY: 17AN XY: 67953
GnomAD4 exome AF: 0.000249 AC: 274AN: 1098233Hom.: 0 Cov.: 32 AF XY: 0.000253 AC XY: 92AN XY: 363591
GnomAD4 genome ? AF: 0.000162 AC: 18AN: 111062Hom.: 0 Cov.: 22 AF XY: 0.000210 AC XY: 7AN XY: 33278
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | NLGN4X: BS2 - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 20, 2014 | - - |
Autism, susceptibility to, X-linked 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jul 08, 2019 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2017 | This alteration is classified as likely 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at