chrY-12786501-C-CT

Variant names:

• chrY-12786501-C-CT
• rs149106583
• NM_004654.4:c.3283-5dupT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_004654.4(USP9Y):​c.3283-5dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00027 (0 hom., 5 hem., cov: 0)
  • Exomes 𝑓: 0.000042 (0 hom. 10 hem.)
  • Failed GnomAD Quality Control
• Consequence: USP9Y NM_004654.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 0 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High Hemizygotes in GnomAdExome4 at 10 YL gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004654.4. 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
	USP9Y	NM_004654.4	MANE Select	c.3283-5dupT		splice_region intron	N/A	NP_004645.2	O00507-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP9Y	ENST00000338981.7	TSL:1 MANE Select	c.3283-21_3283-20insT		intron	N/A	ENSP00000342812.3	O00507-1
	USP9Y	ENST00000651177.1		c.3283-21_3283-20insT		intron	N/A	ENSP00000498372.1	O00507-1
	USP9Y	ENST00000857541.1		c.3283-21_3283-20insT		intron	N/A	ENSP00000527600.1

Frequencies

GnomAD3 genomes AF: 0.000272 AC: 5 AN: 18352 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.000565

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.339 AC: 396 AN: 1167 AF XY: 0.339

Gnomad AFR exome AF: 0.151

Gnomad AMR exome AF: 0.713

Gnomad ASJ exome AF: 0.296

Gnomad EAS exome AF: 0.0149

Gnomad FIN exome AF: 0.0318

Gnomad NFE exome AF: 0.416

Gnomad OTH exome AF: 0.214

GnomAD4 exome AF: 0.0000424 AC: 10 AN: 236074 Hom.: 0 Cov.: 0 AF XY: 0.0000424 AC XY: 10 AN XY: 236074

African (AFR) AF: 0.00 AC: 0 AN: 5207

American (AMR) AF: 0.000168 AC: 1 AN: 5938

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5097

East Asian (EAS) AF: 0.00 AC: 0 AN: 8054

South Asian (SAS) AF: 0.000143 AC: 3 AN: 21010

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9200

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1051

European-Non Finnish (NFE) AF: 0.0000351 AC: 6 AN: 170807

Other (OTH) AF: 0.00 AC: 0 AN: 9710

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000272 AC: 5 AN: 18352 Hom.: 0 Cov.: 0 AF XY: 0.000272 AC XY: 5 AN XY: 18352

African (AFR) AF: 0.00 AC: 0 AN: 4188

American (AMR) AF: 0.00 AC: 0 AN: 2132

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 449

East Asian (EAS) AF: 0.00 AC: 0 AN: 626

South Asian (SAS) AF: 0.00 AC: 0 AN: 842

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 824

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 36

European-Non Finnish (NFE) AF: 0.000565 AC: 5 AN: 8844

Other (OTH) AF: 0.00 AC: 0 AN: 244

Alfa AF: 0.233 Hom.: 57

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs149106583; hg19: chrY-14898435;