chrY-12580293-T-C

Variant names:

• chrY-12580293-T-C
• rs7892988
• ENST00000457658.6:n.653+34043T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-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 the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Hemizygotes in GnomAd4 at 622 YL gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457658.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP9Y	ENST00000457658.6	TSL:2	n.653+34043T>C		intron	N/A

Frequencies

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

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

African (AFR) AF: 0.00408 AC: 35 AN: 8571

American (AMR) AF: 0.0407 AC: 144 AN: 3540

Ashkenazi Jewish (ASJ) AF: 0.00784 AC: 6 AN: 765

East Asian (EAS) AF: 0.000787 AC: 1 AN: 1270

South Asian (SAS) AF: 0.0122 AC: 18 AN: 1476

European-Finnish (FIN) AF: 0.000606 AC: 2 AN: 3301

Middle Eastern (MID) AF: 0.139 AC: 10 AN: 72

European-Non Finnish (NFE) AF: 0.0276 AC: 372 AN: 13477

Other (OTH) AF: 0.0174 AC: 8 AN: 461

Alfa AF: 0.188 Hom.: 177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.5
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs7892988; hg19: chrY-14692227;