rs6786075

chr3-173915081-G-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+107249G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,084 control chromosomes in the GnomAD database, including 6,813 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 0.28 (6813 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: NLGN1 NM_001365925.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

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-AS1 (HGNC:40676): (NLGN1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NLGN1	NM_001365925.2	c.706+107249G>T		intron_variant		ENST00000695368.1
NLGN1-AS1	NR_046664.1	n.272-92C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NLGN1	ENST00000695368.1	c.706+107249G>T		intron_variant			NM_001365925.2	A1
NLGN1-AS1	ENST00000423873.5	n.272-92C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42757 AN: 151962 Hom.: 6787 Cov.: 33

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.271

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.282 AC: 42812 AN: 152080 Hom.: 6813 Cov.: 33 AF XY: 0.281 AC XY: 20871 AN XY: 74340

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.267

Alfa AF: 0.235 Hom.: 2139

Bravo AF: 0.280

Asia WGS AF: 0.254 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.6
Dann	Benign	0.34

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: rs6786075; hg19: chr3-173632871;