dbSNP rs9341278: UTY:c.1569+33C>T (chrY-13357844-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_001258249.2(UTY):c.1569+33C>T variant causes a intron 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 0.086 ( 0 hom., 2824 hem., cov: 0)

Exomes 𝑓: 0.035 ( 0 hom. 11246 hem. )

Consequence

UTY
NM_001258249.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.46

Publications

12 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BS1

Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0855 (2824/33011) while in subpopulation EAS AF = 0.055 (70/1273). AF 95% confidence interval is 0.0446. There are 0 homozygotes in GnomAd4. There are 2824 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High Hemizygotes in GnomAd4 at 2824 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001258249.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UTY	NM_001258249.2	MANE Select	c.1569+33C>T	intron	N/A	NP_001245178.1	F5H8B4
UTY	NM_001400170.1		c.1413+33C>T	intron	N/A	NP_001387099.1
UTY	NM_001400171.1		c.1368+33C>T	intron	N/A	NP_001387100.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UTY	ENST00000545955.6	TSL:1 MANE Select	c.1569+33C>T	intron	N/A	ENSP00000442047.2	F5H8B4
UTY	ENST00000382896.9	TSL:1	c.1503+33C>T	intron	N/A	ENSP00000372352.5	A0A8C8KHL4
UTY	ENST00000617789.5	TSL:1	c.1434+33C>T	intron	N/A	ENSP00000483735.1	A0A087X0Y2

Frequencies

GnomAD3 genomes

AF:

0.0857

AC:

2824

AN:

32946

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000704

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000552

Gnomad ASJ

AF:

0.00131

Gnomad EAS

AF:

0.0549

Gnomad SAS

AF:

0.000660

Gnomad FIN

AF:

0.757

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0314

Gnomad OTH

AF:

0.0368

GnomAD2 exomes

AF:

0.0727

AC:

4038

AN:

55510

AF XY:

0.0727

show subpopulations

Gnomad AFR exome

AF:

0.000778

Gnomad AMR exome

AF:

0.00163

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0418

Gnomad FIN exome

AF:

0.698

Gnomad NFE exome

AF:

0.0169

Gnomad OTH exome

AF:

0.0546

GnomAD4 exome

AF:

0.0352

AC:

11246

AN:

319520

Hom.:

Cov.:

AF XY:

0.0352

AC XY:

11246

AN XY:

319520

show subpopulations

African (AFR)

AF:

0.000475

AC:

AN:

6322

American (AMR)

AF:

0.00165

AC:

AN:

9067

Ashkenazi Jewish (ASJ)

AF:

0.000312

AC:

AN:

6409

East Asian (EAS)

AF:

0.0284

AC:

258

AN:

9100

South Asian (SAS)

AF:

0.000726

AC:

AN:

30314

European-Finnish (FIN)

AF:

0.662

AC:

8301

AN:

12541

Middle Eastern (MID)

AF:

0.00196

AC:

AN:

1533

European-Non Finnish (NFE)

AF:

0.00974

AC:

2254

AN:

231384

Other (OTH)

AF:

0.0302

AC:

388

AN:

12850

Age Distribution

Exome Hom

Variant carriers

144

192

240

<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:

0.0855

AC:

2824

AN:

33011

Hom.:

Cov.:

AF XY:

0.0855

AC XY:

2824

AN XY:

33011

show subpopulations

African (AFR)

AF:

0.000700

AC:

AN:

8577

American (AMR)

AF:

0.000551

AC:

AN:

3631

Ashkenazi Jewish (ASJ)

AF:

0.00131

AC:

AN:

762

East Asian (EAS)

AF:

0.0550

AC:

AN:

1273

South Asian (SAS)

AF:

0.000658

AC:

AN:

1519

European-Finnish (FIN)

AF:

0.757

AC:

2304

AN:

3043

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0314

AC:

423

AN:

13456

Other (OTH)

AF:

0.0365

AC:

AN:

466

Age Distribution

Genome Hom

Variant carriers

126

168

210

<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:

0.0126

Hom.:

392

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.016

(source)

DANN

Benign

0.65

PhyloP100

-2.5

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over