NM_004654.4:c.3283-5delT

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_004654.4(USP9Y):​c.3283-5delT 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 0.43 (0 hom., 7807 hem., cov: 0)
  • Exomes 𝑓: 0.035 (0 hom. 3692 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

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.3283-5delT		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.3283-20delT		intron	N/A	ENSP00000342812.3	O00507-1
	USP9Y	ENST00000651177.1		c.3283-20delT		intron	N/A	ENSP00000498372.1	O00507-1
	USP9Y	ENST00000857541.1		c.3283-20delT		intron	N/A	ENSP00000527600.1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 7807 AN: 18236 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.917

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.459

GnomAD4 exome AF: 0.0354 AC: 3692 AN: 104182 Hom.: 0 Cov.: 0 AF XY: 0.0354 AC XY: 3692 AN XY: 104182

African (AFR) AF: 0.232 AC: 159 AN: 685

American (AMR) AF: 0.0151 AC: 42 AN: 2779

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 75 AN: 907

East Asian (EAS) AF: 0.504 AC: 130 AN: 258

South Asian (SAS) AF: 0.0264 AC: 211 AN: 8005

European-Finnish (FIN) AF: 0.226 AC: 249 AN: 1103

Middle Eastern (MID) AF: 0.395 AC: 87 AN: 220

European-Non Finnish (NFE) AF: 0.0298 AC: 2585 AN: 86621

Other (OTH) AF: 0.0427 AC: 154 AN: 3604

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.428 AC: 7807 AN: 18234 Hom.: 0 Cov.: 0 AF XY: 0.428 AC XY: 7807 AN XY: 18234

African (AFR) AF: 0.682 AC: 2844 AN: 4172

American (AMR) AF: 0.248 AC: 527 AN: 2126

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 316 AN: 446

East Asian (EAS) AF: 0.971 AC: 597 AN: 615

South Asian (SAS) AF: 0.365 AC: 304 AN: 832

European-Finnish (FIN) AF: 0.845 AC: 684 AN: 809

Middle Eastern (MID) AF: 0.912 AC: 31 AN: 34

European-Non Finnish (NFE) AF: 0.268 AC: 2354 AN: 8792

Other (OTH) AF: 0.459 AC: 111 AN: 242

Alfa AF: 0.109 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;