dbSNP rs2032674: UTY:c.966-59A>G (chrY-13360045-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001258249.2(UTY):c.966-59A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0643 in 324,808 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.11 ( 0 hom., 3630 hem., cov: 0)

Exomes 𝑓: 0.059 ( 0 hom. 17247 hem. )

Consequence

UTY
NM_001258249.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.146

Publications

5 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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTY	NM_001258249.2 link	c.966-59A>G		intron_variant	Intron 11 of 29	ENST00000545955.6	NP_001245178.1	F4MH35F5H8B4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTY	ENST00000545955.6 link	c.966-59A>G		intron_variant	Intron 11 of 29	1	NM_001258249.2	ENSP00000442047.2		F5H8B4

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

3631

AN:

32188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00227

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00197

Gnomad ASJ

AF:

0.00132

Gnomad EAS

AF:

0.834

Gnomad SAS

AF:

0.0272

Gnomad FIN

AF:

0.747

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0289

Gnomad OTH

AF:

0.0674

GnomAD4 exome

AF:

0.0590

AC:

17247

AN:

292558

Hom.:

AF XY:

0.0590

AC XY:

17247

AN XY:

292558

show subpopulations

African (AFR)

AF:

0.00206

AC:

AN:

5839

American (AMR)

AF:

0.00427

AC:

AN:

7733

Ashkenazi Jewish (ASJ)

AF:

0.000331

AC:

AN:

6043

East Asian (EAS)

AF:

0.693

AC:

6055

AN:

8740

South Asian (SAS)

AF:

0.0128

AC:

357

AN:

27963

European-Finnish (FIN)

AF:

0.672

AC:

7820

AN:

11634

Middle Eastern (MID)

AF:

0.00550

AC:

AN:

1090

European-Non Finnish (NFE)

AF:

0.00995

AC:

2106

AN:

211589

Other (OTH)

AF:

0.0718

AC:

856

AN:

11927

Age Distribution

Exome Hom

Variant carriers

134

268

402

536

670

<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:

0.113

AC:

3630

AN:

32250

Hom.:

Cov.:

AF XY:

0.113

AC XY:

3630

AN XY:

32250

show subpopulations

African (AFR)

AF:

0.00226

AC:

AN:

8419

American (AMR)

AF:

0.00197

AC:

AN:

3555

Ashkenazi Jewish (ASJ)

AF:

0.00132

AC:

AN:

756

East Asian (EAS)

AF:

0.835

AC:

973

AN:

1165

South Asian (SAS)

AF:

0.0272

AC:

AN:

1436

European-Finnish (FIN)

AF:

0.747

AC:

2178

AN:

2916

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0289

AC:

384

AN:

13269

Other (OTH)

AF:

0.0649

AC:

AN:

447

Age Distribution

Genome Hom

Variant carriers

116

174

232

290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

5.7

(source)

DANN

Benign

0.17

PhyloP100

0.15

Mutation Taster

=100/0

polymorphism

(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