rs10522049
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_181332.3(NLGN4X):c.473-52467A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 111,964 control chromosomes in the GnomAD database, including 127 homozygotes. There are 1,616 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_181332.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLGN4X | NM_181332.3 | c.473-52467A>G | intron_variant | ENST00000381095.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLGN4X | ENST00000381095.8 | c.473-52467A>G | intron_variant | 1 | NM_181332.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0491 AC: 5496AN: 111906Hom.: 126 Cov.: 23 AF XY: 0.0471 AC XY: 1606AN XY: 34094
GnomAD4 genome ? AF: 0.0492 AC: 5510AN: 111964Hom.: 127 Cov.: 23 AF XY: 0.0473 AC XY: 1616AN XY: 34162
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at