Variant Y-12812934-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_004654.4(USP9Y):c.4491C>T(p.Pro1497=) 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 0.0023 ( 0 hom., 77 hem., cov: 0)

Exomes 𝑓: 0.0015 ( 0 hom. 558 hem. )

Consequence

USP9Y
NM_004654.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.907

Variant links:

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]

USP9Y links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant Y-12812934-C-T is Benign according to our data. Variant chrY-12812934-C-T is described in ClinVar as [Benign]. Clinvar id is 1269192.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.907 with no splicing effect.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00229 (77/33692) while in subpopulation EAS AF= 0.0579 (75/1296). AF 95% confidence interval is 0.0473. There are 0 homozygotes in gnomad4. There are 77 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd4 at 77 YL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
USP9Y	NM_004654.4 linkuse as main transcript	c.4491C>T	p.Pro1497=	synonymous_variant	31/46	ENST00000338981.7
USP9Y	XM_047442772.1 linkuse as main transcript	c.4491C>T	p.Pro1497=	synonymous_variant	31/46
USP9Y	XM_047442771.1 linkuse as main transcript	c.4257C>T	p.Pro1419=	synonymous_variant	30/45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP9Y	ENST00000338981.7 linkuse as main transcript	c.4491C>T	p.Pro1497=	synonymous_variant	31/46	1	NM_004654.4	P1	O00507-1
USP9Y	ENST00000651177.1 linkuse as main transcript	c.4491C>T	p.Pro1497=	synonymous_variant	33/48			P1	O00507-1
USP9Y	ENST00000426564.6 linkuse as main transcript	n.4503C>T		non_coding_transcript_exon_variant	29/44	2

Frequencies

GnomAD3 genomes

AF:

0.00229

AC:

AN:

33630

Hom.:

Cov.:

AF XY:

0.00229

AC XY:

AN XY:

33630

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0578

Gnomad SAS

AF:

0.000651

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00211

GnomAD3 exomes

AF:

0.00482

AC:

327

AN:

67885

Hom.:

AF XY:

0.00482

AC XY:

327

AN XY:

67885

show subpopulations

Gnomad AFR exome

AF:

0.000323

Gnomad AMR exome

AF:

0.000559

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0696

Gnomad SAS exome

AF:

0.000347

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00187

GnomAD4 exome

AF:

0.00154

AC:

558

AN:

362757

Hom.:

Cov.:

AF XY:

0.00154

AC XY:

558

AN XY:

362757

show subpopulations

Gnomad4 AFR exome

AF:

0.000142

Gnomad4 AMR exome

AF:

0.000631

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0520

Gnomad4 SAS exome

AF:

0.000561

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000372

Gnomad4 OTH exome

AF:

0.00273

GnomAD4 genome

AF:

0.00229

AC:

AN:

33692

Hom.:

Cov.:

AF XY:

0.00229

AC XY:

AN XY:

33692

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0579

Gnomad4 SAS

AF:

0.000650

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00210

Alfa

AF:

0.00495

Hom.:

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

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

1.9

DANN

Benign

0.36

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

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