rs2032658

Positions:

• chrY-13470103-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001258249.2(UTY):​c.325+18C>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 0.59 (0 hom., 19688 hem., cov: 0)
  • Exomes 𝑓: 0.41 (0 hom. 132953 hem.)
  • Failed GnomAD Quality Control
• Consequence: UTY NM_001258249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTY	NM_001258249.2	c.325+18C>T		intron_variant		ENST00000545955.6	NP_001245178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTY	ENST00000545955.6	c.325+18C>T		intron_variant		1	NM_001258249.2	ENSP00000442047	A1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 19616 AN: 33078 Hom.: 0 Cov.: 0 AF XY: 0.593 AC XY: 19616 AN XY: 33078 FAILED QC

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.958

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.550

GnomAD3 exomes AF: 0.582 AC: 22715 AN: 38996 Hom.: 0 AF XY: 0.582 AC XY: 22715 AN XY: 38996

Gnomad AFR exome AF: 0.810

Gnomad AMR exome AF: 0.602

Gnomad ASJ exome AF: 0.792

Gnomad EAS exome AF: 0.997

Gnomad SAS exome AF: 0.532

Gnomad FIN exome AF: 0.919

Gnomad NFE exome AF: 0.439

Gnomad OTH exome AF: 0.563

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.412 AC: 132953 AN: 322489 Hom.: 0 Cov.: 0 AF XY: 0.412 AC XY: 132953 AN XY: 322489

Gnomad4 AFR exome AF: 0.856

Gnomad4 AMR exome AF: 0.585

Gnomad4 ASJ exome AF: 0.791

Gnomad4 EAS exome AF: 0.998

Gnomad4 SAS exome AF: 0.533

Gnomad4 FIN exome AF: 0.913

Gnomad4 NFE exome AF: 0.323

Gnomad4 OTH exome AF: 0.481

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.594 AC: 19688 AN: 33142 Hom.: 0 Cov.: 0 AF XY: 0.594 AC XY: 19688 AN XY: 33142

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.557

Alfa AF: 0.413 Hom.: 15228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.26

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: rs2032658; hg19: chrY-15581983;