rs1882409

Positions:

• chrX-6215771-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000381095.8(NLGN4X):​c.-306+12770C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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:
  • Genomes: 𝑓 0.65 (17171 hom., 20907 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: NLGN4X ENST00000381095.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504

Genes affected

NLGN4X (HGNC:14287): (neuroligin 4 X-linked) This gene encodes a member of the type-B carboxylesterase/lipase protein family. The encoded protein belongs to a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. The encoded protein interacts with discs large homolog 4 (DLG4). Mutations in this gene have been associated with autism and Asperger syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NLGN4X	NM_181332.3	c.-306+12770C>T		intron_variant		ENST00000381095.8	NP_851849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NLGN4X	ENST00000381095.8	c.-306+12770C>T		intron_variant		1	NM_181332.3	ENSP00000370485	P4

Frequencies

GnomAD3 genomes AF: 0.649 AC: 71440 AN: 110056 Hom.: 17162 Cov.: 22 AF XY: 0.646 AC XY: 20850 AN XY: 32288

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.615

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.649 AC: 71507 AN: 110114 Hom.: 17171 Cov.: 22 AF XY: 0.646 AC XY: 20907 AN XY: 32356

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.614

Alfa AF: 0.589 Hom.: 62561

Bravo AF: 0.657

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1882409; hg19: chrX-6133812;