3-173767581-C-T

Variant names:

• chr3-173767581-C-T
• rs976683
• NM_001365925.2:c.554-40099C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365925.2(NLGN1):​c.554-40099C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,726 control chromosomes in the GnomAD database, including 30,368 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 0.61 (30368 hom., cov: 32)
• Consequence: NLGN1 NM_001365925.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 8 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NLGN1	NM_001365925.2	c.554-40099C>T		intron_variant	Intron 3 of 6	ENST00000695368.1	NP_001352854.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NLGN1	ENST00000695368.1	c.554-40099C>T		intron_variant	Intron 3 of 6		NM_001365925.2	ENSP00000511841.1
NLGN1	ENST00000415045.2	c.554-32712C>T		intron_variant	Intron 3 of 7	1		ENSP00000410374.2
NLGN1	ENST00000361589.8	c.494-40099C>T		intron_variant	Intron 2 of 5	1		ENSP00000354541.4
NLGN1	ENST00000457714.5	c.494-40099C>T		intron_variant	Intron 3 of 6	1		ENSP00000392500.1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93269 AN: 151610 Hom.: 30368 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.615 AC: 93291 AN: 151726 Hom.: 30368 Cov.: 32 AF XY: 0.614 AC XY: 45574 AN XY: 74176

African (AFR) AF: 0.415 AC: 17179 AN: 41374

American (AMR) AF: 0.635 AC: 9677 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2319 AN: 3460

East Asian (EAS) AF: 0.338 AC: 1746 AN: 5162

South Asian (SAS) AF: 0.490 AC: 2359 AN: 4810

European-Finnish (FIN) AF: 0.801 AC: 8441 AN: 10532

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49417 AN: 67846

Other (OTH) AF: 0.601 AC: 1265 AN: 2104

Alfa AF: 0.686 Hom.: 127996

Bravo AF: 0.599

Asia WGS AF: 0.412 AC: 1427 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.63
PhyloP100		-1.6
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: rs976683; hg19: chr3-173485371;