chrX-71147912-C-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_181303.2(NLGN3):c.163C>T(p.Arg55Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000913 in 1,095,414 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_181303.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLGN3 | NM_181303.2 | c.163C>T | p.Arg55Ter | stop_gained | 2/8 | ENST00000358741.4 | |
LOC124905197 | XR_007068262.1 | n.1106+2371G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLGN3 | ENST00000358741.4 | c.163C>T | p.Arg55Ter | stop_gained | 2/8 | 5 | NM_181303.2 | A1 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome AF: 9.13e-7 AC: 1AN: 1095414Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 361080
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
Autism, susceptibility to, X-linked 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | Feb 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at