chr14-19428657-G-A
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001005356.3(POTEG):c.695C>T(p.Pro232Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000474 in 1,203,378 control chromosomes in the GnomAD database, including 19 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000045 ( 1 hom., cov: 16)
Exomes 𝑓: 0.000047 ( 19 hom. )
Failed GnomAD Quality Control
Consequence
POTEG
NM_001005356.3 missense
NM_001005356.3 missense
Scores
2
4
11
Clinical Significance
Conservation
PhyloP100: 6.00
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAdExome4 at 19 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POTEG | NM_001005356.3 | c.695C>T | p.Pro232Leu | missense_variant | 3/11 | ENST00000547848.5 | |
POTEG | NR_027480.2 | n.747C>T | non_coding_transcript_exon_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POTEG | ENST00000547848.5 | c.695C>T | p.Pro232Leu | missense_variant | 3/11 | 1 | NM_001005356.3 | P1 | |
POTEG | ENST00000622767.4 | c.695C>T | p.Pro232Leu | missense_variant, NMD_transcript_variant | 3/12 | 1 | |||
POTEG | ENST00000547722.1 | c.695C>T | p.Pro232Leu | missense_variant, NMD_transcript_variant | 3/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 5AN: 111014Hom.: 1 Cov.: 16 FAILED QC
GnomAD3 genomes
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GnomAD4 exome AF: 0.0000474 AC: 57AN: 1203378Hom.: 19 Cov.: 30 AF XY: 0.0000553 AC XY: 33AN XY: 597162
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000450 AC: 5AN: 111014Hom.: 1 Cov.: 16 AF XY: 0.0000562 AC XY: 3AN XY: 53426
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
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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 | Jun 22, 2023 | The c.695C>T (p.P232L) alteration is located in exon 3 (coding exon 3) of the POTEG gene. This alteration results from a C to T substitution at nucleotide position 695, causing the proline (P) at amino acid position 232 to be replaced by a leucine (L). 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
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D
Sift
Benign
T
Sift4G
Uncertain
T
Vest4
MutPred
Gain of catalytic residue at N233 (P = 0.0011);
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