chr1-13262644-C-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001013407.5(PRAMEF5):c.964C>G(p.Gln322Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 2)
Consequence
PRAMEF5
NM_001013407.5 missense
NM_001013407.5 missense
Scores
3
12
Clinical Significance
Conservation
PhyloP100: -0.170
Genes affected
PRAMEF5 (HGNC:27995): (PRAME family member 5) Predicted to be involved in several processes, including negative regulation of apoptotic process; negative regulation of transcription, DNA-templated; and positive regulation of cell population proliferation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.12069121).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRAMEF5 | NM_001013407.5 | c.964C>G | p.Gln322Glu | missense_variant | 4/4 | ENST00000622421.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRAMEF5 | ENST00000622421.3 | c.964C>G | p.Gln322Glu | missense_variant | 4/4 | 1 | NM_001013407.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 2
GnomAD3 genomes
Cov.:
2
GnomAD4 exome Cov.: 4
GnomAD4 exome
Cov.:
4
GnomAD4 genome Cov.: 2
GnomAD4 genome
Cov.:
2
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 09, 2021 | The c.964C>G (p.Q322E) alteration is located in exon 4 (coding exon 3) of the PRAMEF5 gene. This alteration results from a C to G substitution at nucleotide position 964, causing the glutamine (Q) at amino acid position 322 to be replaced by a glutamic acid (E). 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
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
N
PrimateAI
Uncertain
T
Sift4G
Uncertain
D
Vest4
MVP
ClinPred
T
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.