Y-12793060-T-C

Position:

• chrY-12793060-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000338981.7(USP9Y):​c.3842T>C​(p.Val1281Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/17 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 ENST00000338981.7 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.08

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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.053465337).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
USP9Y	NM_004654.4	c.3842T>C	p.Val1281Ala	missense_variant	27/46	ENST00000338981.7	NP_004645.2
USP9Y	XM_047442772.1	c.3842T>C	p.Val1281Ala	missense_variant	27/46		XP_047298728.1
USP9Y	XM_047442771.1	c.3608T>C	p.Val1203Ala	missense_variant	26/45		XP_047298727.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP9Y	ENST00000338981.7	c.3842T>C	p.Val1281Ala	missense_variant	27/46	1	NM_004654.4	ENSP00000342812	P1
USP9Y	ENST00000651177.1	c.3842T>C	p.Val1281Ala	missense_variant	29/48			ENSP00000498372	P1
USP9Y	ENST00000426564.6	n.3854T>C		non_coding_transcript_exon_variant	25/44	2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 4

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

Juno Genomics, Hangzhou Juno Genomics, Inc

-

PM2_Supporting+PP3 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.40	T
BayesDel_noAF	Benign	-0.81
CADD	Benign	15
DANN	Benign	0.20
DEOGEN2	Benign	0.0018	T
FATHMM_MKL	Benign	0.59	D
LIST_S2	Benign	0.73	T
M_CAP	Uncertain	0.091	D
MetaRNN	Benign	0.053	T
MutationAssessor	Benign	0.0	N
PROVEAN	Benign	0.020	N
Sift	Benign	0.85	T
Sift4G	Benign	0.94	T
Polyphen		0.0	B
Vest4		0.026
MVP		0.44
MPC		0.0059
GERP RS		2.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.10
gMVP		0.25

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrY-14904993;