chrY-13479565-T-A

Variant names:

• chrY-13479565-T-A
• rs9341273
• NM_001258249.2:c.101A>T

Variant summary

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

The NM_001258249.2(UTY):​c.101A>T​(p.Glu34Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000030 (0 hom., 1 hem., cov: 0)
  • Exomes 𝑓: 0.000036 (0 hom. 13 hem.)
  • Failed GnomAD Quality Control
• Consequence: UTY NM_001258249.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12
• Publications: 4 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 -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.10066876).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTY	NM_001258249.2	MANE Select	c.101A>T	p.Glu34Val	missense	Exon 1 of 30	NP_001245178.1
	UTY	NM_001400170.1		c.101A>T	p.Glu34Val	missense	Exon 1 of 29	NP_001387099.1
	UTY	NM_001400171.1		c.101A>T	p.Glu34Val	missense	Exon 1 of 29	NP_001387100.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTY	ENST00000545955.6	TSL:1 MANE Select	c.101A>T	p.Glu34Val	missense	Exon 1 of 30	ENSP00000442047.2
	UTY	ENST00000382896.9	TSL:1	c.101A>T	p.Glu34Val	missense	Exon 1 of 30	ENSP00000372352.5
	UTY	ENST00000617789.5	TSL:1	c.101A>T	p.Glu34Val	missense	Exon 1 of 29	ENSP00000483735.1

Frequencies

GnomAD3 genomes AF: 0.0000304 AC: 1 AN: 32868 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000120

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000740 AC: 5 AN: 67535 AF XY: 0.0000740

Gnomad AFR exome AF: 0.000325

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000665

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000317

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000358 AC: 13 AN: 363443 Hom.: 0 Cov.: 0 AF XY: 0.0000358 AC XY: 13 AN XY: 363443

African (AFR) AF: 0.000141 AC: 1 AN: 7075

American (AMR) AF: 0.00 AC: 0 AN: 9511

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6745

East Asian (EAS) AF: 0.000316 AC: 3 AN: 9485

South Asian (SAS) AF: 0.00 AC: 0 AN: 32093

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12876

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1631

European-Non Finnish (NFE) AF: 0.0000297 AC: 8 AN: 269735

Other (OTH) AF: 0.0000700 AC: 1 AN: 14292

GnomAD4 genome AF: 0.0000304 AC: 1 AN: 32868 Hom.: 0 Cov.: 0 AF XY: 0.0000304 AC XY: 1 AN XY: 32868

African (AFR) AF: 0.000120 AC: 1 AN: 8361

American (AMR) AF: 0.00 AC: 0 AN: 3602

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 756

East Asian (EAS) AF: 0.00 AC: 0 AN: 1224

South Asian (SAS) AF: 0.00 AC: 0 AN: 1476

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3314

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 73

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 13394

Other (OTH) AF: 0.00 AC: 0 AN: 452

Alfa AF: 0.0000367 Hom.: 22

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000534 AC: 1

ExAC AF: 0.0000865 AC: 6

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.43	T
BayesDel_noAF	Benign	-0.49
CADD	Benign	16
DANN	Benign	0.89
DEOGEN2	Benign	0.11	T
FATHMM_MKL	Benign	0.41	N
LIST_S2	Uncertain	0.88	D
M_CAP	Uncertain	0.18	D
MetaRNN	Benign	0.10	T
MutationAssessor	Benign	0.34	N
PhyloP100		2.1
PROVEAN	Pathogenic	-5.0	D
Sift	Uncertain	0.014	D
Sift4G	Benign	0.068	T
Polyphen		0.077	B
Vest4		0.16
MVP		0.043
GERP RS		-0.97
PromoterAI		-0.087	Neutral
Varity_R		0.36
gMVP		0.39
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs9341273; hg19: chrY-15591445;