rs4844285

Positions:

• chrX-71150394-G-A

Variant summary

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

The NM_181303.2(NLGN3):​c.517+1489G>A 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 0.57 (14085 hom., 18045 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: NLGN3 NM_181303.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304

Genes affected

NLGN3 (HGNC:14289): (neuroligin 3) This gene encodes a member of 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. Mutations in this gene may be associated with autism and Asperger syndrome. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Oct 2009]

LOC124905197 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NLGN3	NM_181303.2	c.517+1489G>A		intron_variant		ENST00000358741.4	NP_851820.1
LOC124905197	XR_007068262.1	n.1014-19C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NLGN3	ENST00000358741.4	c.517+1489G>A		intron_variant		5	NM_181303.2	ENSP00000351591	A1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 62917 AN: 110237 Hom.: 14082 Cov.: 22 AF XY: 0.554 AC XY: 17988 AN XY: 32481

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.593

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: 0.571 AC: 62976 AN: 110291 Hom.: 14085 Cov.: 22 AF XY: 0.554 AC XY: 18045 AN XY: 32545

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.600

Alfa AF: 0.493 Hom.: 32829

Bravo AF: 0.596

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.68

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: rs4844285; hg19: chrX-70370244;