chrY-13478462-T-G

Position:

• chrY-13478462-T-G

Variant summary

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

The ENST00000545955.6(UTY):​c.216+792A>C 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., 19203 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: UTY ENST00000545955.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.92

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=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTY	NM_001258249.2	c.216+792A>C		intron_variant		ENST00000545955.6	NP_001245178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTY	ENST00000545955.6	c.216+792A>C		intron_variant		1	NM_001258249.2	ENSP00000442047	A1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 19135 AN: 32257 Hom.: 0 Cov.: 0 AF XY: 0.593 AC XY: 19135 AN XY: 32257 FAILED QC

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.557

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.594 AC: 19203 AN: 32315 Hom.: 0 Cov.: 0 AF XY: 0.594 AC XY: 19203 AN XY: 32315

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.564

Alfa AF: 0.398 Hom.: 16829

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.097

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: rs17307070; hg19: chrY-15590342;