Y-13357844-G-A
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Variant summary
Our verdict is Benign. Variant got -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
NM_001258249.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.46
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 -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 male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Hemizygotes in GnomAd4 at 2824 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UTY | NM_001258249.2 | c.1569+33C>T | intron_variant | ENST00000545955.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTY | ENST00000545955.6 | c.1569+33C>T | intron_variant | 1 | NM_001258249.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0857 AC: 2824AN: 32946Hom.: 0 Cov.: 0 AF XY: 0.0857 AC XY: 2824AN XY: 32946
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GnomAD3 exomes AF: 0.0727 AC: 4038AN: 55510Hom.: 0 AF XY: 0.0727 AC XY: 4038AN XY: 55510
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GnomAD4 exome AF: 0.0352 AC: 11246AN: 319520Hom.: 0 Cov.: 0 AF XY: 0.0352 AC XY: 11246AN XY: 319520
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GnomAD4 genome AF: 0.0855 AC: 2824AN: 33011Hom.: 0 Cov.: 0 AF XY: 0.0855 AC XY: 2824AN XY: 33011
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at