Y-12678428-T-G

Variant names:

• chrY-12678428-T-G
• rs72609647
• ENST00000440408.5:n.421-8085T>G

Variant summary

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

The ENST00000440408.5(USP9Y):​n.421-8085T>G 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 0.0049 (0 hom., 166 hem., cov: 0)
• Consequence: USP9Y ENST00000440408.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 3 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]

TTTY15 (HGNC:18567): (testis expressed transcript, Y-linked 15)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440408.5. 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
	TTTY15	NR_001545.3		n.403-8085T>G		intron	N/A
	TTTY15	NR_174085.1		n.356-8085T>G		intron	N/A
	TTTY15	NR_174086.1		n.356-8085T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP9Y	ENST00000440408.5	TSL:1	n.421-8085T>G		intron	N/A
	USP9Y	ENST00000651177.1		c.-200-8085T>G		intron	N/A	ENSP00000498372.1
	USP9Y	ENST00000417071.1	TSL:2	n.218-8085T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00490 AC: 167 AN: 34048 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00172

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000265

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00632

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

GnomAD4 genome AF: 0.00487 AC: 166 AN: 34112 Hom.: 0 Cov.: 0 AF XY: 0.00487 AC XY: 166 AN XY: 34112

African (AFR) AF: 0.00171 AC: 15 AN: 8785

American (AMR) AF: 0.000265 AC: 1 AN: 3774

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 765

East Asian (EAS) AF: 0.115 AC: 147 AN: 1276

South Asian (SAS) AF: 0.00 AC: 0 AN: 1563

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3516

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 70

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 13668

Other (OTH) AF: 0.00628 AC: 3 AN: 478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.24
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs72609647; hg19: chrY-14790357;