NM_001365925.2:c.707-182148C>T

Variant names:

• chr3-174093167-C-T
• rs16833234
• NM_001365925.2:c.707-182148C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001365925.2(NLGN1):​c.707-182148C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,064 control chromosomes in the GnomAD database, including 2,612 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 0.18 (2612 hom., cov: 32)
• Consequence: NLGN1 NM_001365925.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.674
• Publications: 2 publications found

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]

NLGN1 Gene-Disease associations (from GenCC):

• autism, susceptibility to, 20

  Inheritance: Unknown, AD Classification: MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NLGN1	NM_001365925.2	c.707-182148C>T		intron_variant	Intron 4 of 6	ENST00000695368.1	NP_001352854.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NLGN1	ENST00000695368.1	c.707-182148C>T		intron_variant	Intron 4 of 6		NM_001365925.2	ENSP00000511841.1
NLGN1	ENST00000415045.2	c.767-182148C>T		intron_variant	Intron 5 of 7	1		ENSP00000410374.2
NLGN1	ENST00000361589.8	c.647-182148C>T		intron_variant	Intron 3 of 5	1		ENSP00000354541.4
NLGN1	ENST00000457714.5	c.647-182148C>T		intron_variant	Intron 4 of 6	1		ENSP00000392500.1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27053 AN: 151946 Hom.: 2609 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.178 AC: 27078 AN: 152064 Hom.: 2612 Cov.: 32 AF XY: 0.182 AC XY: 13557 AN XY: 74340

African (AFR) AF: 0.125 AC: 5189 AN: 41516

American (AMR) AF: 0.208 AC: 3177 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3468

East Asian (EAS) AF: 0.377 AC: 1950 AN: 5178

South Asian (SAS) AF: 0.231 AC: 1115 AN: 4818

European-Finnish (FIN) AF: 0.208 AC: 2196 AN: 10562

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11810 AN: 67940

Other (OTH) AF: 0.187 AC: 394 AN: 2110

Alfa AF: 0.174 Hom.: 4380

Bravo AF: 0.173

Asia WGS AF: 0.325 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	16
DANN	Benign	0.77
PhyloP100		0.67
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16833234; hg19: chr3-173810957;