X-5892715-C-T
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_181332.3(NLGN4X):c.*102G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 1,112,611 control chromosomes in the GnomAD database, including 41,117 homozygotes. There are 106,097 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 3_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- X-linked complex neurodevelopmental disorderInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
- autism, susceptibility to, X-linked 2Inheritance: XL Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLGN4X | NM_181332.3 | c.*102G>A | 3_prime_UTR_variant | Exon 6 of 6 | ENST00000381095.8 | NP_851849.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.378 AC: 41590AN: 110091Hom.: 6558 Cov.: 22 show subpopulations
GnomAD4 exome AF: 0.308 AC: 309113AN: 1002466Hom.: 34559 Cov.: 19 AF XY: 0.311 AC XY: 94316AN XY: 302982 show subpopulations
GnomAD4 genome AF: 0.378 AC: 41630AN: 110145Hom.: 6558 Cov.: 22 AF XY: 0.363 AC XY: 11781AN XY: 32451 show subpopulations
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at