rs2032666

chrY-13325684-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001258249.2(UTY):c.2964+537G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00456 in 33,565 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0046 (0 hom., 153 hem., cov: 0)
• Consequence: UTY NM_001258249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.055 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTY	NM_001258249.2	c.2964+537G>A		intron_variant		ENST00000545955.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UTY	ENST00000545955.6	c.2964+537G>A		intron_variant		1	NM_001258249.2	A1

Frequencies

GnomAD3 genomes AF: 0.00457 AC: 153 AN: 33496 Hom.: 0 Cov.: 0 AF XY: 0.00457 AC XY: 153 AN XY: 33496

Gnomad AFR AF: 0.000348

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000547

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0656

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000520

Gnomad OTH AF: 0.00210

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

GnomAD4 genome AF: 0.00456 AC: 153 AN: 33565 Hom.: 0 Cov.: 0 AF XY: 0.00456 AC XY: 153 AN XY: 33565

Gnomad4 AFR AF: 0.000345

Gnomad4 AMR AF: 0.000546

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0664

Gnomad4 SAS AF: 0.0358

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000520

Gnomad4 OTH AF: 0.00208

Alfa AF: 0.0263 Hom.: 330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.6
Dann	Benign	0.35

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: rs2032666; hg19: chrY-15437564;