chr22-31712779-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_173566.3(PRR14L):c.5060C>A(p.Pro1687His) variant causes a missense change. The variant allele was found at a frequency of 0.00000429 in 1,399,622 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000043 ( 0 hom. )
Consequence
PRR14L
NM_173566.3 missense
NM_173566.3 missense
Scores
1
6
12
Clinical Significance
Conservation
PhyloP100: 3.68
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRR14L | NM_173566.3 | c.5060C>A | p.Pro1687His | missense_variant | 4/9 | ENST00000327423.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR14L | ENST00000327423.11 | c.5060C>A | p.Pro1687His | missense_variant | 4/9 | 5 | NM_173566.3 | P1 | |
PRR14L | ENST00000431684.1 | c.1067C>A | p.Pro356His | missense_variant, NMD_transcript_variant | 1/5 | 2 | |||
PRR14L | ENST00000330495.8 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000429 AC: 6AN: 1399622Hom.: 0 Cov.: 34 AF XY: 0.00000290 AC XY: 2AN XY: 690296
GnomAD4 exome
AF:
AC:
6
AN:
1399622
Hom.:
Cov.:
34
AF XY:
AC XY:
2
AN XY:
690296
Gnomad4 AFR exome
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Gnomad4 ASJ exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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Gnomad4 OTH exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2023 | The c.5060C>A (p.P1687H) alteration is located in exon 4 (coding exon 3) of the PRR14L gene. This alteration results from a C to A substitution at nucleotide position 5060, causing the proline (P) at amino acid position 1687 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Pathogenic
D
REVEL
Benign
Sift
Benign
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Gain of helix (P = 0.027);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.