rs9341278

chrY-13357844-G-A

Variant summary

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

The NM_001258249.2(UTY):c.1569+33C>T 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 0.086 (0 hom., 2824 hem., cov: 0)
  • Exomes 𝑓: 0.035 (0 hom. 11246 hem.)
• Consequence: UTY NM_001258249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

Genes affected

UTY (HGNC:12638): (ubiquitously transcribed tetratricopeptide repeat containing, Y-linked) This gene encodes a protein containing tetratricopeptide repeats which are thought to be involved in protein-protein interactions. The encoded protein is also a minor histocompatibility antigen which may induce graft rejection of male stem cell grafts. A large number of alternatively spliced transcripts have been observed for this gene, but the full length nature of some of these variants has not been determined. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0855 (2824/33011) while in subpopulation EAS AF= 0.055 (70/1273). AF 95% confidence interval is 0.0446. There are 0 homozygotes in gnomad4. There are 2824 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Hemizygotes in GnomAd at 2824 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTY	NM_001258249.2	c.1569+33C>T		intron_variant		ENST00000545955.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UTY	ENST00000545955.6	c.1569+33C>T		intron_variant		1	NM_001258249.2	A1

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 2824 AN: 32946 Hom.: 0 Cov.: 0 AF XY: 0.0857 AC XY: 2824 AN XY: 32946

Gnomad AFR AF: 0.000704

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000552

Gnomad ASJ AF: 0.00131

Gnomad EAS AF: 0.0549

Gnomad SAS AF: 0.000660

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0314

Gnomad OTH AF: 0.0368

GnomAD3 exomes AF: 0.0727 AC: 4038 AN: 55510 Hom.: 0 AF XY: 0.0727 AC XY: 4038 AN XY: 55510

Gnomad AFR exome AF: 0.000778

Gnomad AMR exome AF: 0.00163

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0418

Gnomad SAS exome AF: 0.000514

Gnomad FIN exome AF: 0.698

Gnomad NFE exome AF: 0.0169

Gnomad OTH exome AF: 0.0546

GnomAD4 exome AF: 0.0352 AC: 11246 AN: 319520 Hom.: 0 Cov.: 0 AF XY: 0.0352 AC XY: 11246 AN XY: 319520

Gnomad4 AFR exome AF: 0.000475

Gnomad4 AMR exome AF: 0.00165

Gnomad4 ASJ exome AF: 0.000312

Gnomad4 EAS exome AF: 0.0284

Gnomad4 SAS exome AF: 0.000726

Gnomad4 FIN exome AF: 0.662

Gnomad4 NFE exome AF: 0.00974

Gnomad4 OTH exome AF: 0.0302

GnomAD4 genome AF: 0.0855 AC: 2824 AN: 33011 Hom.: 0 Cov.: 0 AF XY: 0.0855 AC XY: 2824 AN XY: 33011

Gnomad4 AFR AF: 0.000700

Gnomad4 AMR AF: 0.000551

Gnomad4 ASJ AF: 0.00131

Gnomad4 EAS AF: 0.0550

Gnomad4 SAS AF: 0.000658

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.0314

Gnomad4 OTH AF: 0.0365

Alfa AF: 0.0152 Hom.: 335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.016
Dann	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs9341278; hg19: chrY-15469724; COSMIC: COSV58870942; COSMIC: COSV58870942;