11-64648559-C-A

Variant names:

• chr11-64648559-C-A
• rs72925197
• NM_015080.4:c.3283+175G>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_015080.4(NRXN2):​c.3283+175G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0234 in 152,282 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.023 (66 hom., cov: 32)
• Consequence: NRXN2 NM_015080.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.399

Genes affected

NRXN2 (HGNC:8009): (neurexin 2) This gene encodes a member of the neurexin gene family. The products of these genes function as cell adhesion molecules and receptors in the vertebrate nervous system. These genes utilize two promoters. The majority of transcripts are produced from the upstream promoter and encode alpha-neurexin isoforms while a smaller number of transcripts are produced from the downstream promoter and encode beta-neuresin isoforms. The alpha-neurexins contain epidermal growth factor-like (EGF-like) sequences and laminin G domains, and have been shown to interact with neurexophilins. The beta-neurexins lack EGF-like sequences and contain fewer laminin G domains than alpha-neurexins. Alternative splicing and the use of alternative promoters may generate thousands of transcript variants (PMID: 12036300, PMID: 11944992).[provided by RefSeq, Jun 2010]

NRXN2-AS1 (HGNC:40416): (NRXN2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP6: Variant 11-64648559-C-A is Benign according to our data. Variant chr11-64648559-C-A is described in ClinVar as [Benign]. Clinvar id is 1232789.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0234 (3559/152282) while in subpopulation NFE AF= 0.0353 (2401/67996). AF 95% confidence interval is 0.0341. There are 66 homozygotes in gnomad4. There are 1767 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 3559 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN2	NM_015080.4	c.3283+175G>T		intron_variant	Intron 16 of 22	ENST00000265459.11	NP_055895.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN2	ENST00000265459.11	c.3283+175G>T		intron_variant	Intron 16 of 22	5	NM_015080.4	ENSP00000265459.5
NRXN2	ENST00000704782.1	c.3292+175G>T		intron_variant	Intron 15 of 21			ENSP00000516031.1
NRXN2	ENST00000704781.1	c.3292+175G>T		intron_variant	Intron 15 of 21			ENSP00000516029.1

Frequencies

GnomAD3 genomes AF: 0.0234 AC: 3559 AN: 152164 Hom.: 66 Cov.: 32

Gnomad AFR AF: 0.00664

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.00798

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00704

Gnomad FIN AF: 0.0644

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0353

Gnomad OTH AF: 0.00907

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

GnomAD4 genome AF: 0.0234 AC: 3559 AN: 152282 Hom.: 66 Cov.: 32 AF XY: 0.0237 AC XY: 1767 AN XY: 74456

Gnomad4 AFR AF: 0.00662

Gnomad4 AMR AF: 0.00790

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00726

Gnomad4 FIN AF: 0.0644

Gnomad4 NFE AF: 0.0353

Gnomad4 OTH AF: 0.00898

Alfa AF: 0.0315 Hom.: 15

Bravo AF: 0.0176

Asia WGS AF: 0.00404 AC: 14 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 21, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	11
DANN	Benign	0.80

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: rs72925197; hg19: chr11-64416031;