Genetic Variant UTY:p.Arg1066His (chrY-13323634-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_001258249.2(UTY):c.3197G>A(p.Arg1066His) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00021 ( 0 hom., 7 hem., cov: 0)

Exomes 𝑓: 0.00021 ( 0 hom. 75 hem. )

Failed GnomAD Quality Control

Consequence

UTY
NM_001258249.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.41

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 -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.1578125).

BP6

Variant Y-13323634-C-T is Benign according to our data. Variant chrY-13323634-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2595555.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTY	NM_001258249.2 link	c.3197G>A	p.Arg1066His	missense_variant	Exon 21 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.3197G>A	p.Arg1066His	missense_variant	Exon 21 of 30	1	NM_001258249.2	ENSP00000442047.2		F5H8B4

Frequencies

GnomAD3 genomes

AF:

0.000211

AC:

AN:

33162

Hom.:

Cov.:

AF XY:

0.000211

AC XY:

AN XY:

33162

show subpopulations

Gnomad AFR

AF:

0.000236

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:

0.000372

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000148

AC:

AN:

67753

Hom.:

AF XY:

0.000148

AC XY:

AN XY:

67753

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000316

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000207

AC:

AN:

362755

Hom.:

Cov.:

AF XY:

0.000207

AC XY:

AN XY:

362755

show subpopulations

Gnomad4 AFR exome

AF:

0.000141

Gnomad4 AMR exome

AF:

0.000105

Gnomad4 ASJ exome

AF:

0.000149

Gnomad4 EAS exome

AF:

0.000105

Gnomad4 SAS exome

AF:

0.0000312

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000253

Gnomad4 OTH exome

AF:

0.000140

GnomAD4 genome

AF:

0.000211

AC:

AN:

33162

Hom.:

Cov.:

AF XY:

0.000211

AC XY:

AN XY:

33162

show subpopulations

Gnomad4 AFR

AF:

0.000236

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:

0.000372

Gnomad4 OTH

AF:

0.00

ExAC

AF:

0.0000287

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Jun 22, 2023

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.071

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.76

DEOGEN2

Benign

0.12

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

FATHMM_MKL

Benign

0.44

LIST_S2

Benign

0.77

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

M_CAP

Benign

0.045

MetaRNN

Benign

0.16

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

MutationAssessor

Benign

0.90

.;.;.;.;.;.;.;.;L;.;L;L

PROVEAN

Benign

-1.7

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

Sift

Benign

0.39

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

Sift4G

Benign

0.13

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

Polyphen

0.0070, 0.037

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

Vest4

0.15

MVP

0.068

GERP RS

-1.5

Varity_R

0.090

gMVP

0.55

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over