Y-13323634-C-T
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
NM_001258249.2 missense
Scores
10
Clinical Significance
Conservation
PhyloP100: 2.41
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]
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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 GnomAd at 7 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UTY | NM_001258249.2 | c.3197G>A | p.Arg1066His | missense_variant | 21/30 | ENST00000545955.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTY | ENST00000545955.6 | c.3197G>A | p.Arg1066His | missense_variant | 21/30 | 1 | NM_001258249.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000211 AC: 7AN: 33162Hom.: 0 Cov.: 0 AF XY: 0.000211 AC XY: 7AN XY: 33162
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GnomAD3 exomes AF: 0.000148 AC: 10AN: 67753Hom.: 0 AF XY: 0.000148 AC XY: 10AN XY: 67753
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000207 AC: 75AN: 362755Hom.: 0 Cov.: 0 AF XY: 0.000207 AC XY: 75AN XY: 362755
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.000211 AC: 7AN: 33162Hom.: 0 Cov.: 0 AF XY: 0.000211 AC XY: 7AN XY: 33162
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2023 | 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T;T;T;T;T;T;T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T
MutationTaster
Benign
D;D;D;D;D;D;D
Sift4G
Benign
T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
0.0070, 0.037
.;.;.;.;.;.;.;.;B;.;.;B
Vest4
MVP
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at