Y-12793053-C-G

Position:

• chrY-12793053-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_004654.4(USP9Y):​c.3835C>G​(p.Leu1279Val) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: USP9Y NM_004654.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.41

Genes affected

USP9Y (HGNC:12633): (ubiquitin specific peptidase 9 Y-linked) This gene is a member of the peptidase C19 family. It encodes a protein that is similar to ubiquitin-specific proteases, which cleave the ubiquitin moiety from ubiquitin-fused precursors and ubiquitinylated proteins. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.08068937).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
USP9Y	NM_004654.4	c.3835C>G	p.Leu1279Val	missense_variant	27/46	ENST00000338981.7
USP9Y	XM_047442772.1	c.3835C>G	p.Leu1279Val	missense_variant	27/46
USP9Y	XM_047442771.1	c.3601C>G	p.Leu1201Val	missense_variant	26/45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP9Y	ENST00000338981.7	c.3835C>G	p.Leu1279Val	missense_variant	27/46	1	NM_004654.4	P1
USP9Y	ENST00000651177.1	c.3835C>G	p.Leu1279Val	missense_variant	29/48			P1
USP9Y	ENST00000426564.6	n.3847C>G		non_coding_transcript_exon_variant	25/44	2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Spermatogenic failure, Y-linked, 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Revvity Omics, Revvity

Jan 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	19
DANN	Benign	0.090
DEOGEN2	Benign	0.0013	T
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.28	T
M_CAP	Uncertain	0.11	D
MetaRNN	Benign	0.081	T
MutationAssessor	Benign	1.1	L
PROVEAN	Benign	0.38	N
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.061	B
Vest4		0.092
MVP		0.33
MPC		0.0063
GERP RS		2.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.16
gMVP		0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrY-14904986;