dbSNP rs2032654: UTY:p.Ser548Ser (chrY-13355944-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001258249.2(UTY):c.1644T>C(p.Ser548Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.039 ( 0 hom., 1304 hem., cov: 0)

Exomes 𝑓: 0.036 ( 0 hom. 12701 hem. )

Consequence

UTY
NM_001258249.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.10

Publications

11 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP7

Synonymous conserved (PhyloP=2.1 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTY	NM_001258249.2 link	c.1644T>C	p.Ser548Ser	synonymous_variant	Exon 16 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.1644T>C	p.Ser548Ser	synonymous_variant	Exon 16 of 30	1	NM_001258249.2	ENSP00000442047.2		F5H8B4

Frequencies

GnomAD3 genomes

AF:

0.0388

AC:

1304

AN:

33642

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0189

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0876

Gnomad ASJ

AF:

0.237

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.00323

Gnomad FIN

AF:

0.00206

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.0413

Gnomad OTH

AF:

0.0889

GnomAD2 exomes

AF:

0.0375

AC:

1946

AN:

51867

AF XY:

0.0375

show subpopulations

Gnomad AFR exome

AF:

0.0145

Gnomad AMR exome

AF:

0.0594

Gnomad ASJ exome

AF:

0.197

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00250

Gnomad NFE exome

AF:

0.0422

Gnomad OTH exome

AF:

0.0698

GnomAD4 exome

AF:

0.0358

AC:

12701

AN:

355030

Hom.:

Cov.:

AF XY:

0.0358

AC XY:

12701

AN XY:

355030

show subpopulations

African (AFR)

AF:

0.0294

AC:

202

AN:

6862

American (AMR)

AF:

0.0733

AC:

627

AN:

8559

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

1396

AN:

6565

East Asian (EAS)

AF:

0.000324

AC:

AN:

9269

South Asian (SAS)

AF:

0.00682

AC:

207

AN:

30361

European-Finnish (FIN)

AF:

0.00366

AC:

AN:

12569

Middle Eastern (MID)

AF:

0.196

AC:

283

AN:

1445

European-Non Finnish (NFE)

AF:

0.0342

AC:

9071

AN:

265464

Other (OTH)

AF:

0.0621

AC:

866

AN:

13936

Age Distribution

Exome Hom

Variant carriers

308

616

924

1232

1540

<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:

0.0387

AC:

1304

AN:

33705

Hom.:

Cov.:

AF XY:

0.0387

AC XY:

1304

AN XY:

33705

show subpopulations

African (AFR)

AF:

0.0187

AC:

162

AN:

8642

American (AMR)

AF:

0.0874

AC:

323

AN:

3695

Ashkenazi Jewish (ASJ)

AF:

0.237

AC:

182

AN:

767

East Asian (EAS)

AF:

0.000769

AC:

AN:

1301

South Asian (SAS)

AF:

0.00323

AC:

AN:

1550

European-Finnish (FIN)

AF:

0.00206

AC:

AN:

3398

Middle Eastern (MID)

AF:

0.292

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0413

AC:

562

AN:

13601

Other (OTH)

AF:

0.0884

AC:

AN:

464

Age Distribution

Genome Hom

Variant carriers

100

<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:

0.0768

Hom.:

2094

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

(source)

DANN

Benign

0.44

PhyloP100

2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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