rs17307070

Variant names:

• chrY-13478462-T-G
• rs17307070
• NM_001258249.2:c.216+792A>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001258249.2(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 NM_001258249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.92
• Publications: 7 publications found

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=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTY	NM_001258249.2	c.216+792A>C		intron_variant	Intron 2 of 29	ENST00000545955.6	NP_001245178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTY	ENST00000545955.6	c.216+792A>C		intron_variant	Intron 2 of 29	1	NM_001258249.2	ENSP00000442047.2

Frequencies

GnomAD3 genomes AF: 0.593 AC: 19135 AN: 32257 Hom.: 0 Cov.: 0

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

African (AFR) AF: 0.794 AC: 6493 AN: 8173

American (AMR) AF: 0.500 AC: 1756 AN: 3510

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 609 AN: 752

East Asian (EAS) AF: 0.996 AC: 1245 AN: 1250

South Asian (SAS) AF: 0.658 AC: 951 AN: 1445

European-Finnish (FIN) AF: 0.932 AC: 2896 AN: 3106

Middle Eastern (MID) AF: 0.958 AC: 69 AN: 72

European-Non Finnish (NFE) AF: 0.365 AC: 4865 AN: 13332

Other (OTH) AF: 0.564 AC: 261 AN: 463

Alfa AF: 0.438 Hom.: 24842

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
PhyloP100		-3.9
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs17307070; hg19: chrY-15590342;