rs2032658

Variant names:

• chrY-13470103-G-A
• rs2032658
• NM_001258249.2:c.325+18C>T

Variant summary

Our verdict is Likely benign. The variant received -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

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTY	NM_001258249.2	c.325+18C>T		intron_variant	Intron 3 of 29	ENST00000545955.6	NP_001245178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTY	ENST00000545955.6	c.325+18C>T		intron_variant	Intron 3 of 29	1	NM_001258249.2	ENSP00000442047.2

Frequencies

GnomAD3 genomes AF: 0.593 AC: 19616 AN: 33078 Hom.: 0 Cov.: 0

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

GnomAD2 exomes AF: 0.582 AC: 22715 AN: 38996 AF XY: 0.582

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 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 AC: 5221 AN: 6101

Gnomad4 AMR exome AF: 0.585 AC: 3648 AN: 6236

Gnomad4 ASJ exome AF: 0.791 AC: 4552 AN: 5752

Gnomad4 EAS exome AF: 0.998 AC: 8637 AN: 8653

Gnomad4 SAS exome AF: 0.533 AC: 14110 AN: 26470

Gnomad4 FIN exome AF: 0.913 AC: 11047 AN: 12095

Gnomad4 NFE exome AF: 0.323 AC: 78704 AN: 243396

Gnomad4 Remaining exome AF: 0.481 AC: 6088 AN: 12665

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 AC: 0.797552 AN: 0.797552

Gnomad4 AMR AF: 0.506 AC: 0.505674 AN: 0.505674

Gnomad4 ASJ AF: 0.806 AC: 0.806069 AN: 0.806069

Gnomad4 EAS AF: 0.996 AC: 0.996032 AN: 0.996032

Gnomad4 SAS AF: 0.552 AC: 0.551927 AN: 0.551927

Gnomad4 FIN AF: 0.936 AC: 0.936261 AN: 0.936261

Gnomad4 NFE AF: 0.366 AC: 0.365689 AN: 0.365689

Gnomad4 OTH AF: 0.557 AC: 0.557484 AN: 0.557484

Alfa AF: 0.451 Hom.: 21990

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
Mutation Taster		=100/0	polymorphism (auto)

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;