rs1861957

chr14-79707892-C-Achr14-79707892-C-T

Variant summary

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

The NM_001330195.2(NRXN3):c.4014+9955C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,948 control chromosomes in the GnomAD database, including 17,990 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 0.48 (17990 hom., cov: 33)
• Consequence: NRXN3 NM_001330195.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

NRXN3 (HGNC:8010): (neurexin 3) This gene encodes a member of a family of proteins that function in the nervous system as receptors and cell adhesion molecules. Extensive alternative splicing and the use of alternative promoters results in multiple transcript variants and protein isoforms for this gene, but the full-length nature of many of these variants has not been determined. Transcripts that initiate from an upstream promoter encode alpha isoforms, which contain epidermal growth factor-like (EGF-like) sequences and laminin G domains. Transcripts initiating from the downstream promoter encode beta isoforms, which lack EGF-like sequences. Genetic variation at this locus has been associated with a range of behavioral phenotypes, including alcohol dependence and autism spectrum disorder. [provided by RefSeq, Dec 2012]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NRXN3	NM_001330195.2	c.4014+9955C>A		intron_variant		ENST00000335750.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NRXN3	ENST00000335750.7	c.4014+9955C>A		intron_variant		5	NM_001330195.2	P1
	ENST00000553322.1	n.210-38680G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72672 AN: 151830 Hom.: 17972 Cov.: 33

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.479 AC: 72728 AN: 151948 Hom.: 17990 Cov.: 33 AF XY: 0.476 AC XY: 35312 AN XY: 74256

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.442

Alfa AF: 0.452 Hom.: 19616

Bravo AF: 0.484

Asia WGS AF: 0.453 AC: 1571 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.5
Dann	Benign	0.32

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: rs1861957; hg19: chr14-80174235;