Y-12738407-T-C

Variant names:

• chrY-12738407-T-C
• rs2032598
• NM_004654.4:c.1317+98T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004654.4(USP9Y):​c.1317+98T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0391 in 206,460 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.15 (0 hom., 4937 hem., cov: 0)
  • Exomes 𝑓: 0.018 (0 hom. 3132 hem.)
• Consequence: USP9Y NM_004654.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405
• Publications: 8 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP9Y	NM_004654.4	MANE Select	c.1317+98T>C		intron	N/A	NP_004645.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP9Y	ENST00000338981.7	TSL:1 MANE Select	c.1317+98T>C		intron	N/A	ENSP00000342812.3
	USP9Y	ENST00000651177.1		c.1317+98T>C		intron	N/A	ENSP00000498372.1
	USP9Y	ENST00000426564.6	TSL:2	n.1329+98T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 4904 AN: 33310 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00196

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0274

Gnomad NFE AF: 0.00213

Gnomad OTH AF: 0.0807

GnomAD4 exome AF: 0.0181 AC: 3132 AN: 173089 Hom.: 0 AF XY: 0.0181 AC XY: 3132 AN XY: 173089

African (AFR) AF: 0.646 AC: 2659 AN: 4119

American (AMR) AF: 0.0235 AC: 132 AN: 5610

Ashkenazi Jewish (ASJ) AF: 0.000904 AC: 4 AN: 4426

East Asian (EAS) AF: 0.00 AC: 0 AN: 8315

South Asian (SAS) AF: 0.00187 AC: 40 AN: 21334

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10217

Middle Eastern (MID) AF: 0.00840 AC: 8 AN: 952

European-Non Finnish (NFE) AF: 0.000472 AC: 52 AN: 110136

Other (OTH) AF: 0.0297 AC: 237 AN: 7980

GnomAD4 genome AF: 0.148 AC: 4937 AN: 33371 Hom.: 0 Cov.: 0 AF XY: 0.148 AC XY: 4937 AN XY: 33371

African (AFR) AF: 0.569 AC: 4741 AN: 8337

American (AMR) AF: 0.0338 AC: 124 AN: 3674

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 769

East Asian (EAS) AF: 0.00 AC: 0 AN: 1323

South Asian (SAS) AF: 0.00196 AC: 3 AN: 1534

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3375

Middle Eastern (MID) AF: 0.0278 AC: 2 AN: 72

European-Non Finnish (NFE) AF: 0.00213 AC: 29 AN: 13596

Other (OTH) AF: 0.0802 AC: 38 AN: 474

Alfa AF: 0.0997 Hom.: 4353

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.7
DANN	Benign	0.54
PhyloP100		0.41

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

Other links and lift over

dbSNP: rs2032598; hg19: chrY-14850341;