X-5892974-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_181332.3(NLGN4X):c.2294G>A(p.Arg765His) variant causes a missense change. The variant allele was found at a frequency of 0.0000141 in 1,209,347 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R765R) has been classified as Likely benign.
Frequency
Consequence
NM_181332.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLGN4X | NM_181332.3 | c.2294G>A | p.Arg765His | missense_variant | Exon 6 of 6 | ENST00000381095.8 | NP_851849.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000900 AC: 1AN: 111079Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33279
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183525Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67953
GnomAD4 exome AF: 0.0000146 AC: 16AN: 1098268Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 4AN XY: 363622
GnomAD4 genome AF: 0.00000900 AC: 1AN: 111079Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33279
ClinVar
Submissions by phenotype
not provided Uncertain:1
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Autism, susceptibility to, X-linked 2 Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at