chr15-44665812-A-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_001387263.1(PATL2):c.*141T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00349 in 1,522,328 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0027 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0036 ( 10 hom. )
Consequence
PATL2
NM_001387263.1 3_prime_UTR
NM_001387263.1 3_prime_UTR
Scores
1
8
Clinical Significance
Conservation
PhyloP100: 0.535
Genes affected
PATL2 (HGNC:33630): (PAT1 homolog 2) Predicted to enable RNA binding activity. Predicted to be involved in P-body assembly and deadenylation-dependent decapping of nuclear-transcribed mRNA. Predicted to act upstream of or within negative regulation of cytoplasmic mRNA processing body assembly. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0039250255).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00268 (408/152290) while in subpopulation NFE AF= 0.00469 (319/68018). AF 95% confidence interval is 0.00427. There are 0 homozygotes in gnomad4. There are 185 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High Homozygotes in GnomAdExome4 at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PATL2 | NM_001387263.1 | c.*141T>A | 3_prime_UTR_variant | 18/18 | ENST00000682850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PATL2 | ENST00000682850.1 | c.*141T>A | 3_prime_UTR_variant | 18/18 | NM_001387263.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00268 AC: 408AN: 152172Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00226 AC: 291AN: 128840Hom.: 1 AF XY: 0.00225 AC XY: 156AN XY: 69280
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GnomAD4 exome AF: 0.00358 AC: 4911AN: 1370038Hom.: 10 Cov.: 30 AF XY: 0.00340 AC XY: 2293AN XY: 675086
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GnomAD4 genome AF: 0.00268 AC: 408AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.00248 AC XY: 185AN XY: 74462
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
N;N;N
PROVEAN
Benign
N
Sift
Pathogenic
D
MVP
GERP RS
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