Variant chrY-14824201-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001365588.1(NLGN4Y):c.699C>T(p.Thr233=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0053 ( 0 hom., 175 hem., cov: 0)

Exomes 𝑓: 0.0040 ( 0 hom. 1435 hem. )

Failed GnomAD Quality Control

Consequence

NLGN4Y
NM_001365588.1 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.652

Variant links:

Genes affected

NLGN4Y (HGNC:15529): (neuroligin 4 Y-linked) This gene encodes a type I membrane protein that belongs to the family of neuroligins, which are cell adhesion molecules present at the postsynaptic side of the synapse, and may be essential for the formation of functional synapses. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Mar 2011]

NLGN4Y links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant Y-14824201-C-T is Benign according to our data. Variant chrY-14824201-C-T is described in ClinVar as [Benign]. Clinvar id is 777318.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.652 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 175 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NLGN4Y	NM_001365588.1 linkuse as main transcript	c.699C>T	p.Thr233=	synonymous_variant	5/7	ENST00000684976.1	NP_001352517.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NLGN4Y	ENST00000684976.1 linkuse as main transcript	c.699C>T	p.Thr233=	synonymous_variant	5/7		NM_001365588.1	ENSP00000510011	A1

Frequencies

GnomAD3 genomes

AF:

0.00529

AC:

175

AN:

33090

Hom.:

Cov.:

AF XY:

0.00529

AC XY:

175

AN XY:

33090

show subpopulations

Gnomad AFR

AF:

0.000356

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0155

Gnomad ASJ

AF:

0.0695

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000682

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0274

Gnomad NFE

AF:

0.00415

Gnomad OTH

AF:

0.00899

GnomAD3 exomes

AF:

0.00588

AC:

396

AN:

67358

Hom.:

AF XY:

0.00588

AC XY:

396

AN XY:

67358

show subpopulations

Gnomad AFR exome

AF:

0.000978

Gnomad AMR exome

AF:

0.00970

Gnomad ASJ exome

AF:

0.0542

Gnomad EAS exome

AF:

0.000221

Gnomad SAS exome

AF:

0.00218

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00445

Gnomad OTH exome

AF:

0.0113

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00395

AC:

1435

AN:

363052

Hom.:

Cov.:

AF XY:

0.00395

AC XY:

1435

AN XY:

363052

show subpopulations

Gnomad4 AFR exome

AF:

0.00212

Gnomad4 AMR exome

AF:

0.00958

Gnomad4 ASJ exome

AF:

0.0575

Gnomad4 EAS exome

AF:

0.000211

Gnomad4 SAS exome

AF:

0.00231

Gnomad4 FIN exome

AF:

0.0000777

Gnomad4 NFE exome

AF:

0.00252

Gnomad4 OTH exome

AF:

0.00911

GnomAD4 genome

AF:

0.00528

AC:

175

AN:

33155

Hom.:

Cov.:

AF XY:

0.00528

AC XY:

175

AN XY:

33155

show subpopulations

Gnomad4 AFR

AF:

0.000353

Gnomad4 AMR

AF:

0.0154

Gnomad4 ASJ

AF:

0.0695

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000680

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00415

Gnomad4 OTH

AF:

0.00893

Alfa

AF:

0.0214

Hom.:

302

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 07, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

4.9

DANN

Benign

0.56

Splicing

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