Genetic Variant NM_001258249.2:c.101A>G (chrY-13479565-T-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

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

Publications

4 publications found

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 was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

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

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.:

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

GnomAD2 exomes

AF:

0.000948

AC:

AN:

67535

AF XY:

0.000948

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 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

African (AFR)

AF:

0.000283

AC:

AN:

7075

American (AMR)

AF:

0.00284

AC:

AN:

9511

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6745

East Asian (EAS)

AF:

0.00822

AC:

AN:

9485

South Asian (SAS)

AF:

0.00106

AC:

AN:

32093

European-Finnish (FIN)

AF:

0.0000777

AC:

AN:

12876

Middle Eastern (MID)

AF:

0.00368

AC:

AN:

1631

European-Non Finnish (NFE)

AF:

0.000619

AC:

167

AN:

269735

Other (OTH)

AF:

0.000700

AC:

AN:

14292

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000972

AC:

AN:

32928

Hom.:

Cov.:

AF XY:

0.000972

AC XY:

AN XY:

32928

show subpopulations

African (AFR)

AF:

0.000475

AC:

AN:

8413

American (AMR)

AF:

0.00610

AC:

AN:

3609

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

756

East Asian (EAS)

AF:

0.00327

AC:

AN:

1223

South Asian (SAS)

AF:

0.00

AC:

AN:

1479

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3314

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0000747

AC:

AN:

13393

Other (OTH)

AF:

0.00220

AC:

AN:

455

Age Distribution

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000808

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

(source)

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;.

PhyloP100

2.1

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

PromoterAI

-0.016

Neutral

(source)

Varity_R

0.14

gMVP

0.26

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over