Y-14608133-T-C

Variant names:

• chrY-14608133-T-C
• rs28819996
• NM_001365588.1:c.-111-13876T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001365588.1(NLGN4Y):​c.-111-13876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.99 (0 hom., 32226 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: NLGN4Y NM_001365588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: YL Classification: LIMITED Submitted by: King Faisal Specialist Hospital and Research Center

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365588.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NLGN4Y	NM_001365588.1	MANE Select	c.-111-13876T>C		intron	N/A	NP_001352517.1
	NLGN4Y	NM_001365584.1		c.-111-13876T>C		intron	N/A	NP_001352513.1
	NLGN4Y	NM_001365586.1		c.-111-13876T>C		intron	N/A	NP_001352515.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NLGN4Y	ENST00000684976.1	MANE Select	c.-111-13876T>C		intron	N/A	ENSP00000510011.1
	NLGN4Y	ENST00000382868.5	TSL:1	c.-99-13888T>C		intron	N/A	ENSP00000372320.1
	NLGN4Y	ENST00000339174.9	TSL:1	c.-111-13876T>C		intron	N/A	ENSP00000342535.5

Frequencies

GnomAD3 genomes AF: 0.993 AC: 32162 AN: 32373 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.995

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.993

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.993 AC: 32226 AN: 32437 Hom.: 0 Cov.: 0 AF XY: 0.993 AC XY: 32226 AN XY: 32437

African (AFR) AF: 0.996 AC: 8262 AN: 8295

American (AMR) AF: 0.995 AC: 3480 AN: 3499

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 754 AN: 754

East Asian (EAS) AF: 1.00 AC: 1211 AN: 1211

South Asian (SAS) AF: 1.00 AC: 1421 AN: 1421

European-Finnish (FIN) AF: 1.00 AC: 3188 AN: 3188

Middle Eastern (MID) AF: 1.00 AC: 70 AN: 70

European-Non Finnish (NFE) AF: 0.989 AC: 13184 AN: 13325

Other (OTH) AF: 0.993 AC: 458 AN: 461

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.7
DANN	Benign	0.36
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs28819996; hg19: chrY-16720013;