chr17-7407154-A-C

Variant names:

• chr17-7407154-A-C
• rs11078674
• ENST00000575301.5:c.-244-858A>C

Variant summary

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

The ENST00000572893.1(NLGN2):​n.256-1306A>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 ENST00000572893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000572893.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NLGN2	ENST00000575301.5	TSL:5	c.-244-858A>C		intron	N/A	ENSP00000461168.1	Q8NFZ4
	NLGN2	ENST00000572893.1	TSL:3	n.256-1306A>C		intron	N/A

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

African (AFR) AF: 0.384 AC: 15879 AN: 41382

American (AMR) AF: 0.475 AC: 7256 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2052 AN: 3468

East Asian (EAS) AF: 0.293 AC: 1513 AN: 5160

South Asian (SAS) AF: 0.473 AC: 2276 AN: 4814

European-Finnish (FIN) AF: 0.659 AC: 6936 AN: 10526

Middle Eastern (MID) AF: 0.483 AC: 140 AN: 290

European-Non Finnish (NFE) AF: 0.687 AC: 46659 AN: 67934

Other (OTH) AF: 0.559 AC: 1176 AN: 2104

Alfa AF: 0.629 Hom.: 45750

Bravo AF: 0.533

Asia WGS AF: 0.388 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11078674; hg19: chr17-7310473;