rs2032654

Positions:

• chrY-13355944-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001258249.2(UTY):​c.1644T>C​(p.Ser548Ser) variant causes a synonymous 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 0.039 (0 hom., 1304 hem., cov: 0)
  • Exomes 𝑓: 0.036 (0 hom. 12701 hem.)
• Consequence: UTY NM_001258249.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10

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]

UTY (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP7: Synonymous conserved (PhyloP=2.1 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTY	NM_001258249.2	c.1644T>C	p.Ser548Ser	synonymous_variant	16/30	ENST00000545955.6	NP_001245178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTY	ENST00000545955.6	c.1644T>C	p.Ser548Ser	synonymous_variant	16/30	1	NM_001258249.2	ENSP00000442047.2

Frequencies

GnomAD3 genomes AF: 0.0388 AC: 1304 AN: 33642 Hom.: 0 Cov.: 0 AF XY: 0.0388 AC XY: 1304 AN XY: 33642

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0876

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.00323

Gnomad FIN AF: 0.00206

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0889

GnomAD3 exomes AF: 0.0375 AC: 1946 AN: 51867 Hom.: 0 AF XY: 0.0375 AC XY: 1946 AN XY: 51867

Gnomad AFR exome AF: 0.0145

Gnomad AMR exome AF: 0.0594

Gnomad ASJ exome AF: 0.197

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00691

Gnomad FIN exome AF: 0.00250

Gnomad NFE exome AF: 0.0422

Gnomad OTH exome AF: 0.0698

GnomAD4 exome AF: 0.0358 AC: 12701 AN: 355030 Hom.: 0 Cov.: 0 AF XY: 0.0358 AC XY: 12701 AN XY: 355030

Gnomad4 AFR exome AF: 0.0294

Gnomad4 AMR exome AF: 0.0733

Gnomad4 ASJ exome AF: 0.213

Gnomad4 EAS exome AF: 0.000324

Gnomad4 SAS exome AF: 0.00682

Gnomad4 FIN exome AF: 0.00366

Gnomad4 NFE exome AF: 0.0342

Gnomad4 OTH exome AF: 0.0621

GnomAD4 genome AF: 0.0387 AC: 1304 AN: 33705 Hom.: 0 Cov.: 0 AF XY: 0.0387 AC XY: 1304 AN XY: 33705

Gnomad4 AFR AF: 0.0187

Gnomad4 AMR AF: 0.0874

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.000769

Gnomad4 SAS AF: 0.00323

Gnomad4 FIN AF: 0.00206

Gnomad4 NFE AF: 0.0413

Gnomad4 OTH AF: 0.0884

Alfa AF: 0.0647 Hom.: 1399

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	13
DANN	Benign	0.44

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: rs2032654; hg19: chrY-15467824;