chrX-5893140-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_181332.3(NLGN4X):c.2128C>T(p.Arg710Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000579 in 1,209,635 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R710H) has been classified as Uncertain significance.
Frequency
Consequence
NM_181332.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLGN4X | NM_181332.3 | c.2128C>T | p.Arg710Cys | missense_variant | 6/6 | ENST00000381095.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLGN4X | ENST00000381095.8 | c.2128C>T | p.Arg710Cys | missense_variant | 6/6 | 1 | NM_181332.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111501Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33695
GnomAD4 exome AF: 0.00000455 AC: 5AN: 1098081Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 363553
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111554Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33758
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 02, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at