chr14-19428559-T-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001005356.3(POTEG):āc.793A>Gā(p.Ile265Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00020 ( 0 hom., cov: 6)
Exomes š: 0.00012 ( 3 hom. )
Failed GnomAD Quality Control
Consequence
POTEG
NM_001005356.3 missense
NM_001005356.3 missense
Scores
1
2
14
Clinical Significance
Conservation
PhyloP100: 2.37
Genes affected
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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=0.11775407).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POTEG | NM_001005356.3 | c.793A>G | p.Ile265Val | missense_variant | 3/11 | ENST00000547848.5 | |
POTEG | NR_027480.2 | n.845A>G | non_coding_transcript_exon_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POTEG | ENST00000547848.5 | c.793A>G | p.Ile265Val | missense_variant | 3/11 | 1 | NM_001005356.3 | P1 | |
POTEG | ENST00000622767.4 | c.793A>G | p.Ile265Val | missense_variant, NMD_transcript_variant | 3/12 | 1 | |||
POTEG | ENST00000547722.1 | c.793A>G | p.Ile265Val | missense_variant, NMD_transcript_variant | 3/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 11AN: 55104Hom.: 0 Cov.: 6 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000121 AC: 121AN: 1002256Hom.: 3 Cov.: 17 AF XY: 0.0000936 AC XY: 47AN XY: 502044
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000200 AC: 11AN: 55104Hom.: 0 Cov.: 6 AF XY: 0.000115 AC XY: 3AN XY: 26026
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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 | Nov 09, 2021 | The c.793A>G (p.I265V) alteration is located in exon 3 (coding exon 3) of the POTEG gene. This alteration results from a A to G substitution at nucleotide position 793, causing the isoleucine (I) at amino acid position 265 to be replaced by a valine (V). 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
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
Sift
Benign
T
Sift4G
Benign
T
Vest4
MutPred
Gain of catalytic residue at K268 (P = 0.001);
MVP
ClinPred
D
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