rs11078674

chr17-7407154-A-C

Variant summary

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

The ENST00000575301.5(NLGN2):c.-244-858A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,854 control chromosomes in the GnomAD database, including 25,216 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 0.56 (25216 hom., cov: 31)
• Consequence: NLGN2 ENST00000575301.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

NLGN2 (HGNC:14290): (neuroligin 2) 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NLGN2	XM_017024897.2	c.-81+1544A>C		intron_variant
NLGN2	XM_047436462.1	c.-244-858A>C		intron_variant
NLGN2	XM_047436463.1	c.-641-461A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NLGN2	ENST00000575301.5	c.-244-858A>C		intron_variant		5		P1
NLGN2	ENST00000572893.1	n.256-1306A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84439 AN: 151734 Hom.: 25208 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.556 AC: 84475 AN: 151854 Hom.: 25216 Cov.: 31 AF XY: 0.549 AC XY: 40745 AN XY: 74178

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.559

Alfa AF: 0.633 Hom.: 6530

Bravo AF: 0.533

Asia WGS AF: 0.388 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	12
Dann	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11078674; hg19: chr17-7310473;