rs9341273

chrY-13479565-T-AchrY-13479565-T-CchrY-13479565-T-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Moderate BS2

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

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 -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.10066876).
• BS2: High Hemizygotes in GnomAdExome at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTY	NM_001258249.2	c.101A>T	p.Glu34Val	missense_variant	1/30	ENST00000545955.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UTY	ENST00000545955.6	c.101A>T	p.Glu34Val	missense_variant	1/30	1	NM_001258249.2	A1

Frequencies

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

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

GnomAD3 exomes AF: 0.0000740 AC: 5 AN: 67535 Hom.: 0 AF XY: 0.0000740 AC XY: 5 AN XY: 67535

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 SAS exome AF: 0.00

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

Gnomad4 AFR exome AF: 0.000141

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000316

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000297

Gnomad4 OTH exome AF: 0.0000700

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

Gnomad4 AFR AF: 0.000120

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000485 Hom.: 17

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 v4.3

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
FATHMM_MKL	Benign	0.41	N
LIST_S2	Uncertain	0.88	D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP	Uncertain	0.18	D
MetaRNN	Benign	0.10	T;T;T;T;T;T;T;T;T;T;T;T;T
MutationTaster	Benign	1.0	N;N;N;N;N;N;N;N
PROVEAN	Pathogenic	-5.0	D;D;D;D;D;.;.;.;D;.;D;D;D
Sift	Uncertain	0.014	D;D;D;D;D;.;.;.;D;.;D;D;D
Sift4G	Benign	0.068	T;T;T;T;T;T;T;T;T;D;T;D;D
Polyphen		0.077, 0.53	.;.;.;.;.;.;.;.;B;.;.;P;.
Vest4		0.16
MVP		0.043
GERP RS		-0.97
Varity_R		0.36
gMVP		0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs9341273; hg19: chrY-15591445;