1-155688110-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000355499.9(YY1AP1):c.-60T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0084 in 1,610,104 control chromosomes in the GnomAD database, including 105 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0072 ( 6 hom., cov: 29)
Exomes 𝑓: 0.0085 ( 99 hom. )
Consequence
YY1AP1
ENST00000355499.9 5_prime_UTR
ENST00000355499.9 5_prime_UTR
Scores
17
Clinical Significance
Conservation
PhyloP100: 1.40
Genes affected
YY1AP1 (HGNC:30935): (YY1 associated protein 1) Predicted to enable transcription coregulator activity. Involved in cell differentiation; cell population proliferation; and regulation of cell cycle. Located in fibrillar center and nucleoplasm. Colocalizes with Ino80 complex. [provided by Alliance of Genome Resources, Apr 2022]
DAP3 (HGNC:2673): (death associated protein 3) Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 28S subunit protein that also participates in apoptotic pathways which are initiated by tumor necrosis factor-alpha, Fas ligand, and gamma interferon. This protein potentially binds ATP/GTP and might be a functional partner of the mitoribosomal protein S27. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. Pseudogenes corresponding to this gene are found on chromosomes 1q and 2q. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0037935078).
BP6
Variant 1-155688110-A-G is Benign according to our data. Variant chr1-155688110-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 782734.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0072 (1096/152288) while in subpopulation NFE AF= 0.00928 (631/68016). AF 95% confidence interval is 0.00868. There are 6 homozygotes in gnomad4. There are 576 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YY1AP1 | NM_139119.3 | c.-60T>C | 5_prime_UTR_variant | 2/11 | ENST00000355499.9 | NP_620830.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YY1AP1 | ENST00000355499.9 | c.-60T>C | 5_prime_UTR_variant | 2/11 | 1 | NM_139119.3 | ENSP00000347686 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00722 AC: 1098AN: 152170Hom.: 6 Cov.: 29
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GnomAD3 exomes AF: 0.00684 AC: 1699AN: 248404Hom.: 12 AF XY: 0.00678 AC XY: 912AN XY: 134596
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GnomAD4 exome AF: 0.00853 AC: 12433AN: 1457816Hom.: 99 Cov.: 30 AF XY: 0.00829 AC XY: 6010AN XY: 724748
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GnomAD4 genome AF: 0.00720 AC: 1096AN: 152288Hom.: 6 Cov.: 29 AF XY: 0.00773 AC XY: 576AN XY: 74474
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | YY1AP1: BP4, BS2 - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 08, 2018 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;N;.
MutationTaster
Benign
D;D;D;D;D;D;D;D;D;D;D;N;N;N;N
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
.;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
0.0
.;.;B;B
Vest4
MVP
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ClinPred
T
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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