rs7051529

chrX-71154354-A-GchrX-71154354-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_181303.2(NLGN3):c.577+818A>G 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 0.55 (13061 hom., 18681 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: NLGN3 NM_181303.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS2: High Homozygotes in GnomAd at 13060 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NLGN3	NM_181303.2	c.577+818A>G		intron_variant		ENST00000358741.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NLGN3	ENST00000358741.4	c.577+818A>G		intron_variant		5	NM_181303.2	A1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 61929 AN: 111715 Hom.: 13060 Cov.: 24 AF XY: 0.549 AC XY: 18622 AN XY: 33925

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.607

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.561

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: 0.555 AC: 61986 AN: 111768 Hom.: 13061 Cov.: 24 AF XY: 0.550 AC XY: 18681 AN XY: 33988

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.569

Alfa AF: 0.488 Hom.: 4529

Bravo AF: 0.576

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.99
Dann	Benign	0.65

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: rs7051529; hg19: chrX-70374204; COSMIC: COSV62445601;