chr17-7252534-C-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000396628.7(ELP5):c.-17C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
ELP5
ENST00000396628.7 5_prime_UTR
ENST00000396628.7 5_prime_UTR
Scores
2
17
Clinical Significance
Conservation
PhyloP100: 0.727
Genes affected
ELP5 (HGNC:30617): (elongator acetyltransferase complex subunit 5) Predicted to contribute to tRNA binding activity. Predicted to be involved in positive regulation of cell migration and tRNA modification. Located in cytosol and nucleoplasm. Part of elongator holoenzyme complex. [provided by Alliance of Genome Resources, Apr 2022]
CTDNEP1 (HGNC:19085): (CTD nuclear envelope phosphatase 1) Enables protein serine/threonine phosphatase activity. Involved in several processes, including positive regulation of triglyceride biosynthetic process; protein dephosphorylation; and protein localization to nucleus. Located in endoplasmic reticulum membrane; lipid droplet; and nuclear membrane. Part of Nem1-Spo7 phosphatase complex. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09118998).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELP5 | NM_203414.3 | c.-17C>T | 5_prime_UTR_variant | 1/8 | ENST00000396628.7 | NP_981959.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ELP5 | ENST00000396628.7 | c.-17C>T | 5_prime_UTR_variant | 1/8 | 1 | NM_203414.3 | ENSP00000379869 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 33
GnomAD3 genomes
AF:
AC:
2
AN:
152198
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249082Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134952
GnomAD3 exomes
AF:
AC:
4
AN:
249082
Hom.:
AF XY:
AC XY:
3
AN XY:
134952
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461524Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727052
GnomAD4 exome
AF:
AC:
5
AN:
1461524
Hom.:
Cov.:
31
AF XY:
AC XY:
4
AN XY:
727052
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74460
GnomAD4 genome
AF:
AC:
2
AN:
152316
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74460
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ExAC
AF:
AC:
2
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2022 | The c.32C>T (p.T11I) alteration is located in exon 1 (coding exon 1) of the ELP5 gene. This alteration results from a C to T substitution at nucleotide position 32, causing the threonine (T) at amino acid position 11 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
.;.;T;.;.;T;T;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;.;T;.;T;.;.;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;L;L;L;L;.;L;L;L
MutationTaster
Benign
N;N;N;N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
.;.;N;.;N;N;.;.;N;.
REVEL
Benign
Sift
Uncertain
.;.;D;.;D;D;.;.;D;.
Sift4G
Benign
T;T;T;T;T;T;T;T;T;T
Polyphen
0.047, 0.14, 0.13
.;.;B;B;B;B;.;B;B;B
Vest4
0.13, 0.13, 0.16, 0.084, 0.075, 0.088
MutPred
Loss of phosphorylation at T11 (P = 0.0087);Loss of phosphorylation at T11 (P = 0.0087);Loss of phosphorylation at T11 (P = 0.0087);Loss of phosphorylation at T11 (P = 0.0087);Loss of phosphorylation at T11 (P = 0.0087);Loss of phosphorylation at T11 (P = 0.0087);Loss of phosphorylation at T11 (P = 0.0087);Loss of phosphorylation at T11 (P = 0.0087);Loss of phosphorylation at T11 (P = 0.0087);Loss of phosphorylation at T11 (P = 0.0087);
MVP
MPC
0.18
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