rs6754640

chr2-50504180-G-Achr2-50504180-G-T

Variant summary

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

The NM_001330078.2(NRXN1):c.2497+2315C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 147,444 control chromosomes in the GnomAD database, including 13,500 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 0.42 (13500 hom., cov: 27)
• Consequence: NRXN1 NM_001330078.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

Genes affected

NRXN1 (HGNC:8008): (neurexin 1) This gene encodes a single-pass type I membrane protein that belongs to the neurexin family. Neurexins are cell-surface receptors that bind neuroligins to form Ca(2+)-dependent neurexin/neuroligin complexes at synapses in the central nervous system. This complex is required for efficient neurotransmission and is involved in the formation of synaptic contacts. Three members of this gene family have been studied in detail and are estimated to generate over 3,000 variants through the use of two alternative promoters (alpha and beta) and extensive alternative splicing in each family member. Recently, a third promoter (gamma) was identified for this gene in the 3' region. Mutations in this gene are associated with Pitt-Hopkins-like syndrome-2 and may contribute to susceptibility to schizophrenia. [provided by RefSeq, Aug 2016]

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 = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NRXN1	NM_001330078.2	c.2497+2315C>T		intron_variant		ENST00000401669.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NRXN1	ENST00000401669.7	c.2497+2315C>T		intron_variant		5	NM_001330078.2	A1

Frequencies

GnomAD3 genomes AF: 0.417 AC: 61416 AN: 147376 Hom.: 13482 Cov.: 27

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.0923

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.537

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.417 AC: 61464 AN: 147444 Hom.: 13500 Cov.: 27 AF XY: 0.415 AC XY: 29690 AN XY: 71592

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.0920

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.415

Alfa AF: 0.379 Hom.: 4272

Bravo AF: 0.400

Asia WGS AF: 0.268 AC: 933 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.1
Dann	Benign	0.44

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: rs6754640; hg19: chr2-50731318;