chrY-13287334-G-T

Variant names:

• chrY-13287334-G-T
• rs15434
• NM_001258249.2:c.4010+10373C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001258249.2(UTY):​c.4010+10373C>A 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: not found (cov: 0)
• Consequence: UTY NM_001258249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.774
• Publications: 2 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]

PSMA6P1 (HGNC:17460): (proteasome subunit alpha 6 pseudogene 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001258249.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTY	NM_001258249.2	MANE Select	c.4010+10373C>A		intron	N/A	NP_001245178.1	F5H8B4
	UTY	NM_001400170.1		c.3854+10373C>A		intron	N/A	NP_001387099.1
	UTY	NM_001400171.1		c.3809+10373C>A		intron	N/A	NP_001387100.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTY	ENST00000545955.6	TSL:1 MANE Select	c.4010+10373C>A		intron	N/A	ENSP00000442047.2	F5H8B4
	UTY	ENST00000382896.9	TSL:1	c.3944+10373C>A		intron	N/A	ENSP00000372352.5	A0A8C8KHL4
	UTY	ENST00000617789.5	TSL:1	c.3875+10373C>A		intron	N/A	ENSP00000483735.1	A0A087X0Y2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	7.9
DANN	Benign	0.90
PhyloP100		0.77

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: rs15434; hg19: chrY-15399214;