dbSNP rs9341273: UTY:p.Glu34Val (chrY-13479565-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. Variant got -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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.12

Variant links:

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]

UTY links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTY	NM_001258249.2 link	c.101A>T	p.Glu34Val	missense_variant	Exon 1 of 30	ENST00000545955.6	NP_001245178.1	F4MH35F5H8B4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTY	ENST00000545955.6 link	c.101A>T	p.Glu34Val	missense_variant	Exon 1 of 30	1	NM_001258249.2	ENSP00000442047.2		F5H8B4

Frequencies

GnomAD3 genomes

AF:

0.0000304

AC:

AN:

32868

Hom.:

Cov.:

AF XY:

0.0000304

AC XY:

AN XY:

32868

show subpopulations

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:

AN:

67535

Hom.:

AF XY:

0.0000740

AC XY:

AN XY:

67535

show subpopulations

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:

AN:

363443

Hom.:

Cov.:

AF XY:

0.0000358

AC XY:

AN XY:

363443

show subpopulations

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:

AN:

32868

Hom.:

Cov.:

AF XY:

0.0000304

AC XY:

AN XY:

32868

show subpopulations

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.:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000534

AC:

ExAC

AF:

0.0000865

AC:

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

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.89

DEOGEN2

Benign

0.11

.;T;.;.;.;.;T;T;T;.;.;.;.

FATHMM_MKL

Benign

0.41

LIST_S2

Uncertain

0.88

D;D;D;D;D;D;D;D;D;D;D;D;D

M_CAP

Uncertain

0.18

MetaRNN

Benign

0.10

T;T;T;T;T;T;T;T;T;T;T;T;T

MutationAssessor

Benign

0.34

.;.;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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over