Y-14579942-G-T

Variant names:

• chrY-14579942-G-T
• rs73621792
• NM_001365588.1:c.-111-42067G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365588.1(NLGN4Y):​c.-111-42067G>T 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 0.14 (0 hom., 4385 hem., cov: 0)
• Consequence: NLGN4Y NM_001365588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 2 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NLGN4Y	NM_001365588.1	MANE Select	c.-111-42067G>T		intron	N/A	NP_001352517.1	B4DHI3
	NLGN4Y	NM_001365584.1		c.-111-42067G>T		intron	N/A	NP_001352513.1	B4DHI3
	NLGN4Y	NM_001365586.1		c.-111-42067G>T		intron	N/A	NP_001352515.1	B4DHI3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NLGN4Y	ENST00000684976.1	MANE Select	c.-111-42067G>T		intron	N/A	ENSP00000510011.1	B4DHI3
	NLGN4Y	ENST00000382868.5	TSL:1	c.-99-42079G>T		intron	N/A	ENSP00000372320.1	A6NMU8
	NLGN4Y	ENST00000339174.9	TSL:1	c.-111-42067G>T		intron	N/A	ENSP00000342535.5	Q8NFZ3-1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 4357 AN: 30340 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0364

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000758

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0286

Gnomad NFE AF: 0.00162

Gnomad OTH AF: 0.0790

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

GnomAD4 genome AF: 0.144 AC: 4385 AN: 30389 Hom.: 0 Cov.: 0 AF XY: 0.144 AC XY: 4385 AN XY: 30389

African (AFR) AF: 0.567 AC: 4213 AN: 7433

American (AMR) AF: 0.0364 AC: 116 AN: 3191

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 726

East Asian (EAS) AF: 0.00 AC: 0 AN: 1191

South Asian (SAS) AF: 0.000756 AC: 1 AN: 1323

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2873

Middle Eastern (MID) AF: 0.0294 AC: 2 AN: 68

European-Non Finnish (NFE) AF: 0.00162 AC: 21 AN: 12968

Other (OTH) AF: 0.0784 AC: 32 AN: 408

Alfa AF: 0.515 Hom.: 1664

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs73621792; hg19: chrY-16691822;