3-173819851-C-T

Position:

• chr3-173819851-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365925.2(NLGN1):​c.706+12019C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,200 control chromosomes in the GnomAD database, including 54,858 homozygotes. 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 0.84 (54858 hom., cov: 33)
• Consequence: NLGN1 NM_001365925.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

NLGN1 (HGNC:14291): (neuroligin 1) 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. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NLGN1	NM_001365925.2	c.706+12019C>T		intron_variant		ENST00000695368.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NLGN1	ENST00000695368.1	c.706+12019C>T		intron_variant			NM_001365925.2	A1
	ENST00000691300.1	n.956C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128101 AN: 152082 Hom.: 54812 Cov.: 33

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.842 AC: 128203 AN: 152200 Hom.: 54858 Cov.: 33 AF XY: 0.834 AC XY: 62090 AN XY: 74418

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.803

Alfa AF: 0.841 Hom.: 27155

Bravo AF: 0.842

Asia WGS AF: 0.548 AC: 1909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.67

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: rs1873038; hg19: chr3-173537641;