Genetic Variant UTY:p.Glu34Gly (chrY-13479565-T-C) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_001258249.2(UTY):c.101A>G(p.Glu34Gly) 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. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00097 ( 0 hom., 32 hem., cov: 0)

Exomes 𝑓: 0.00089 ( 0 hom. 325 hem. )

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 Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0072476566).

BP6

Variant Y-13479565-T-C is Benign according to our data. Variant chrY-13479565-T-C is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAd4 at 32 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTY	NM_001258249.2 link	c.101A>G	p.Glu34Gly	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>G	p.Glu34Gly	missense_variant	Exon 1 of 30	1	NM_001258249.2	ENSP00000442047.2		F5H8B4

Frequencies

GnomAD3 genomes

AF:

0.000943

AC:

AN:

32867

Hom.:

Cov.:

AF XY:

0.000943

AC XY:

AN XY:

32867

show subpopulations

Gnomad AFR

AF:

0.000359

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00611

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00327

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000747

Gnomad OTH

AF:

0.00221

GnomAD3 exomes

AF:

0.000948

AC:

AN:

67535

Hom.:

AF XY:

0.000948

AC XY:

AN XY:

67535

show subpopulations

Gnomad AFR exome

AF:

0.000325

Gnomad AMR exome

AF:

0.00294

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000887

Gnomad SAS exome

AF:

0.00122

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000761

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000894

AC:

325

AN:

363443

Hom.:

Cov.:

AF XY:

0.000894

AC XY:

325

AN XY:

363443

show subpopulations

Gnomad4 AFR exome

AF:

0.000283

Gnomad4 AMR exome

AF:

0.00284

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00822

Gnomad4 SAS exome

AF:

0.00106

Gnomad4 FIN exome

AF:

0.0000777

Gnomad4 NFE exome

AF:

0.000619

Gnomad4 OTH exome

AF:

0.000700

GnomAD4 genome

AF:

0.000972

AC:

AN:

32928

Hom.:

Cov.:

AF XY:

0.000972

AC XY:

AN XY:

32928

show subpopulations

Gnomad4 AFR

AF:

0.000475

Gnomad4 AMR

AF:

0.00610

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00327

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000747

Gnomad4 OTH

AF:

0.00220

Alfa

AF:

0.000824

Hom.:

ExAC

AF:

0.000865

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.67

DEOGEN2

Benign

0.10

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

FATHMM_MKL

Benign

0.31

LIST_S2

Benign

0.72

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

M_CAP

Uncertain

0.12

MetaRNN

Benign

0.0072

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

MutationAssessor

Benign

0.34

.;.;N;.;.;.;.;.;N;N;N;N;.

PROVEAN

Uncertain

-4.2

D;D;D;D;D;.;.;.;D;.;D;D;D

Sift

Benign

0.23

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

Sift4G

Benign

0.40

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

Polyphen

0.0020, 0.013

.;.;.;.;.;.;.;.;B;.;.;B;.

Vest4

0.11

MVP

0.043

GERP RS

-0.97

Varity_R

0.14

gMVP

0.26

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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