NM_004654.4:c.773+131A>C

Variant names:

• chrY-12735858-A-C
• rs2032597
• NM_004654.4:c.773+131A>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.773+131A>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 0.11 (0 hom., 3701 hem., cov: 0)
  • Exomes 𝑓: 0.17 (0 hom. 42134 hem.)
  • Failed GnomAD Quality Control
• Consequence: USP9Y NM_004654.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950
• Publications: 23 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP9Y	NM_004654.4	c.773+131A>C		intron_variant	Intron 8 of 45	ENST00000338981.7	NP_004645.2
USP9Y	XM_047442772.1	c.773+131A>C		intron_variant	Intron 8 of 45		XP_047298728.1
USP9Y	XM_047442771.1	c.539+131A>C		intron_variant	Intron 7 of 44		XP_047298727.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP9Y	ENST00000338981.7	c.773+131A>C		intron_variant	Intron 8 of 45	1	NM_004654.4	ENSP00000342812.3
USP9Y	ENST00000651177.1	c.773+131A>C		intron_variant	Intron 10 of 47			ENSP00000498372.1
USP9Y	ENST00000426564.6	n.785+131A>C		intron_variant	Intron 6 of 43	2

Frequencies

GnomAD3 genomes AF: 0.112 AC: 3702 AN: 32994 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0447

Gnomad AMI AF: 0.0372

Gnomad AMR AF: 0.0686

Gnomad ASJ AF: 0.0327

Gnomad EAS AF: 0.00158

Gnomad SAS AF: 0.00130

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.0837

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.175 AC: 42134 AN: 240915 Hom.: 0 Cov.: 0 AF XY: 0.175 AC XY: 42134 AN XY: 240915

African (AFR) AF: 0.0443 AC: 209 AN: 4719

American (AMR) AF: 0.0583 AC: 334 AN: 5727

Ashkenazi Jewish (ASJ) AF: 0.0304 AC: 156 AN: 5132

East Asian (EAS) AF: 0.00 AC: 0 AN: 8243

South Asian (SAS) AF: 0.00135 AC: 31 AN: 23004

European-Finnish (FIN) AF: 0.251 AC: 2500 AN: 9950

Middle Eastern (MID) AF: 0.0124 AC: 11 AN: 887

European-Non Finnish (NFE) AF: 0.217 AC: 37658 AN: 173191

Other (OTH) AF: 0.123 AC: 1235 AN: 10062

GnomAD4 genome AF: 0.112 AC: 3701 AN: 33058 Hom.: 0 Cov.: 0 AF XY: 0.112 AC XY: 3701 AN XY: 33058

African (AFR) AF: 0.0444 AC: 381 AN: 8577

American (AMR) AF: 0.0682 AC: 245 AN: 3593

Ashkenazi Jewish (ASJ) AF: 0.0327 AC: 25 AN: 764

East Asian (EAS) AF: 0.00158 AC: 2 AN: 1267

South Asian (SAS) AF: 0.00130 AC: 2 AN: 1544

European-Finnish (FIN) AF: 0.154 AC: 493 AN: 3205

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 73

European-Non Finnish (NFE) AF: 0.188 AC: 2507 AN: 13362

Other (OTH) AF: 0.0830 AC: 38 AN: 458

Alfa AF: 0.196 Hom.: 9257

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.40
PhyloP100		-0.95

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2032597; hg19: chrY-14847792;