chr22-31712852-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_173566.3(PRR14L):āc.4987T>Cā(p.Phe1663Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00288 in 1,551,984 control chromosomes in the GnomAD database, including 117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.015 ( 58 hom., cov: 32)
Exomes š: 0.0016 ( 59 hom. )
Consequence
PRR14L
NM_173566.3 missense
NM_173566.3 missense
Scores
4
6
8
Clinical Significance
Conservation
PhyloP100: 4.46
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0049679577).
BP6
Variant 22-31712852-A-G is Benign according to our data. Variant chr22-31712852-A-G is described in ClinVar as [Benign]. Clinvar id is 777687.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRR14L | NM_173566.3 | c.4987T>C | p.Phe1663Leu | missense_variant | 4/9 | ENST00000327423.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR14L | ENST00000327423.11 | c.4987T>C | p.Phe1663Leu | missense_variant | 4/9 | 5 | NM_173566.3 | P1 | |
PRR14L | ENST00000431684.1 | c.994T>C | p.Phe332Leu | missense_variant, NMD_transcript_variant | 1/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0149 AC: 2272AN: 152148Hom.: 58 Cov.: 32
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GnomAD3 exomes AF: 0.00345 AC: 545AN: 157808Hom.: 13 AF XY: 0.00253 AC XY: 211AN XY: 83314
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GnomAD4 exome AF: 0.00157 AC: 2194AN: 1399718Hom.: 59 Cov.: 34 AF XY: 0.00131 AC XY: 903AN XY: 690344
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GnomAD4 genome AF: 0.0149 AC: 2272AN: 152266Hom.: 58 Cov.: 32 AF XY: 0.0142 AC XY: 1057AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Gain of phosphorylation at S1664 (P = 0.1078);
MVP
MPC
ClinPred
T
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