rs9786706

Variant names:

• chrY-12586994-C-T
• rs9786706
• ENST00000457658.6:n.653+40744C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000457658.6(USP9Y):​n.653+40744C>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 0.0024 (0 hom., 80 hem., cov: 0)
• Consequence: USP9Y ENST00000457658.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS2: High Hemizygotes in GnomAd4 at 80 YL gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457658.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP9Y	ENST00000457658.6	TSL:2	n.653+40744C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00245 AC: 80 AN: 32707 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000239

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.00345

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00327

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00244 AC: 80 AN: 32768 Hom.: 0 Cov.: 0 AF XY: 0.00244 AC XY: 80 AN XY: 32768

African (AFR) AF: 0.000238 AC: 2 AN: 8421

American (AMR) AF: 0.00344 AC: 12 AN: 3487

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 755

East Asian (EAS) AF: 0.00 AC: 0 AN: 1239

South Asian (SAS) AF: 0.00 AC: 0 AN: 1443

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3243

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 74

European-Non Finnish (NFE) AF: 0.00328 AC: 44 AN: 13435

Other (OTH) AF: 0.00 AC: 0 AN: 457

Alfa AF: 0.0163 Hom.: 911

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
PhyloP100		0.36

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: rs9786706;

hg19: chrY-14698928;