Y-12786501-CTTTTT-CTT

Variant names:

• chrY-12786501-CTTT-C
• rs149106583
• NM_004654.4:c.3283-7_3283-5delTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_004654.4(USP9Y):​c.3283-7_3283-5delTTT 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: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: USP9Y NM_004654.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988
• 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: Uncertain_significance. The variant received 0 ACMG points.

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.3283-7_3283-5delTTT		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.3283-20_3283-18delTTT		intron	N/A	ENSP00000342812.3	O00507-1
	USP9Y	ENST00000651177.1		c.3283-20_3283-18delTTT		intron	N/A	ENSP00000498372.1	O00507-1
	USP9Y	ENST00000857541.1		c.3283-20_3283-18delTTT		intron	N/A	ENSP00000527600.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 295007 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 295007

African (AFR) AF: 0.00 AC: 0 AN: 5329

American (AMR) AF: 0.00 AC: 0 AN: 7202

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5423

East Asian (EAS) AF: 0.00 AC: 0 AN: 7785

South Asian (SAS) AF: 0.00 AC: 0 AN: 25766

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9091

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1092

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 221582

Other (OTH) AF: 0.00 AC: 0 AN: 11737

GnomAD4 genome Cov.: 0

Alfa AF: 0.00272 Hom.: 57

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.99

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;