X-5892824-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_181332.3(NLGN4X):c.2444G>C(p.Arg815Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000331 in 1,209,227 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 (★).
Frequency
Consequence
NM_181332.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLGN4X | NM_181332.3 | c.2444G>C | p.Arg815Thr | missense_variant | Exon 6 of 6 | ENST00000381095.8 | NP_851849.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000900 AC: 1AN: 111063Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33247
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183309Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67743
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1098164Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363520
GnomAD4 genome AF: 0.00000900 AC: 1AN: 111063Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33247
ClinVar
Submissions by phenotype
not provided Uncertain:1
In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at