rs7892988

Positions:

• chrY-12580293-T-C
• chrY-12580293-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000457658.6(USP9Y):​n.653+34043T>C 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 0.019 (0 hom., 622 hem., cov: 0)
• Consequence: USP9Y ENST00000457658.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0188 (622/33147) while in subpopulation AMR AF= 0.0407 (144/3540). AF 95% confidence interval is 0.0353. There are 0 homozygotes in gnomad4. There are 622 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Hemizygotes in GnomAd4 at 622 YL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP9Y	ENST00000457658.6	n.653+34043T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0187 AC: 620 AN: 33086 Hom.: 0 Cov.: 0 AF XY: 0.0187 AC XY: 620 AN XY: 33086

Gnomad AFR AF: 0.00411

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0408

Gnomad ASJ AF: 0.00784

Gnomad EAS AF: 0.000787

Gnomad SAS AF: 0.0115

Gnomad FIN AF: 0.000606

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0275

Gnomad OTH AF: 0.0175

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

GnomAD4 genome AF: 0.0188 AC: 622 AN: 33147 Hom.: 0 Cov.: 0 AF XY: 0.0188 AC XY: 622 AN XY: 33147

Gnomad4 AFR AF: 0.00408

Gnomad4 AMR AF: 0.0407

Gnomad4 ASJ AF: 0.00784

Gnomad4 EAS AF: 0.000787

Gnomad4 SAS AF: 0.0122

Gnomad4 FIN AF: 0.000606

Gnomad4 NFE AF: 0.0276

Gnomad4 OTH AF: 0.0174

Alfa AF: 0.202 Hom.: 56

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.5

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7892988; hg19: chrY-14692227;