11-59639325-T-G
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_152716.3(PATL1):āc.2108A>Cā(p.Asp703Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000135 in 1,551,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000026 ( 0 hom., cov: 32)
Exomes š: 0.000012 ( 0 hom. )
Consequence
PATL1
NM_152716.3 missense
NM_152716.3 missense
Scores
2
5
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.44
Genes affected
PATL1 (HGNC:26721): (PAT1 homolog 1, processing body mRNA decay factor) Enables poly(G) binding activity and poly(U) RNA binding activity. Involved in P-body assembly and deadenylation-dependent decapping of nuclear-transcribed mRNA. Located in P-body and cytosol. Colocalizes with CCR4-NOT complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.1410383).
BS2
High AC in GnomAdExome4 at 17 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PATL1 | NM_152716.3 | c.2108A>C | p.Asp703Ala | missense_variant | 17/19 | ENST00000300146.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PATL1 | ENST00000300146.10 | c.2108A>C | p.Asp703Ala | missense_variant | 17/19 | 1 | NM_152716.3 | P1 | |
ENST00000661394.1 | n.582T>G | non_coding_transcript_exon_variant | 5/5 | ||||||
ENST00000531108.1 | n.223T>G | non_coding_transcript_exon_variant | 4/4 | 3 | |||||
ENST00000531311.1 | n.65T>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152146Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000445 AC: 7AN: 157348Hom.: 0 AF XY: 0.0000241 AC XY: 2AN XY: 83014
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GnomAD4 exome AF: 0.0000122 AC: 17AN: 1399078Hom.: 0 Cov.: 31 AF XY: 0.00000869 AC XY: 6AN XY: 690092
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74464
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Pathogenic
D
Polyphen
B
Vest4
MutPred
Gain of glycosylation at P704 (P = 0.0746);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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