Variant chrX-5892715-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_181332.3(NLGN4X):c.*102G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 1,112,611 control chromosomes in the GnomAD database, including 41,117 homozygotes. There are 106,097 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 6558 hom., 11781 hem., cov: 22)

Exomes 𝑓: 0.31 ( 34559 hom. 94316 hem. )

Consequence

NLGN4X
NM_181332.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.452

Variant links:

Genes affected

NLGN4X (HGNC:14287): (neuroligin 4 X-linked) This gene encodes a member of the type-B carboxylesterase/lipase protein family. The encoded protein belongs to 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. The encoded protein interacts with discs large homolog 4 (DLG4). Mutations in this gene have been associated with autism and Asperger syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

NLGN4X links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant X-5892715-C-T is Benign according to our data. Variant chrX-5892715-C-T is described in ClinVar as [Benign]. Clinvar id is 1238862.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NLGN4X	NM_181332.3 linkuse as main transcript	c.*102G>A		3_prime_UTR_variant	6/6	ENST00000381095.8	NP_851849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NLGN4X	ENST00000381095.8 linkuse as main transcript	c.*102G>A		3_prime_UTR_variant	6/6	1	NM_181332.3	ENSP00000370485	P4	Q8N0W4-1

Frequencies

GnomAD3 genomes

AF:

0.378

AC:

41590

AN:

110091

Hom.:

6558

Cov.:

AF XY:

0.362

AC XY:

11736

AN XY:

32387

show subpopulations

Gnomad AFR

AF:

0.604

Gnomad AMI

AF:

0.392

Gnomad AMR

AF:

0.316

Gnomad ASJ

AF:

0.307

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.248

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.302

Gnomad OTH

AF:

0.343

GnomAD4 exome

AF:

0.308

AC:

309113

AN:

1002466

Hom.:

34559

Cov.:

AF XY:

0.311

AC XY:

94316

AN XY:

302982

show subpopulations

Gnomad4 AFR exome

AF:

0.616

Gnomad4 AMR exome

AF:

0.280

Gnomad4 ASJ exome

AF:

0.310

Gnomad4 EAS exome

AF:

0.145

Gnomad4 SAS exome

AF:

0.261

Gnomad4 FIN exome

AF:

0.276

Gnomad4 NFE exome

AF:

0.310

Gnomad4 OTH exome

AF:

0.308

GnomAD4 genome

AF:

0.378

AC:

41630

AN:

110145

Hom.:

6558

Cov.:

AF XY:

0.363

AC XY:

11781

AN XY:

32451

show subpopulations

Gnomad4 AFR

AF:

0.604

Gnomad4 AMR

AF:

0.316

Gnomad4 ASJ

AF:

0.307

Gnomad4 EAS

AF:

0.143

Gnomad4 SAS

AF:

0.246

Gnomad4 FIN

AF:

0.256

Gnomad4 NFE

AF:

0.302

Gnomad4 OTH

AF:

0.339

Alfa

AF:

0.329

Hom.:

2075

Bravo

AF:

0.392

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.077

DANN

Benign

0.52

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over