chr3-186080012-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004454.3(ETV5):c.455C>A(p.Pro152Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000722 in 1,550,264 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 0.000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000073 ( 0 hom. )
Consequence
ETV5
NM_004454.3 missense
NM_004454.3 missense
Scores
1
5
12
Clinical Significance
Conservation
PhyloP100: 7.04
Genes affected
ETV5 (HGNC:3494): (ETS variant transcription factor 5) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in cellular response to oxidative stress; negative regulation of transcription by RNA polymerase II; and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.21762297).
BS2
?
High AC in GnomAd at 10 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ETV5 | NM_004454.3 | c.455C>A | p.Pro152Gln | missense_variant | 7/13 | ENST00000306376.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ETV5 | ENST00000306376.10 | c.455C>A | p.Pro152Gln | missense_variant | 7/13 | 1 | NM_004454.3 | P1 | |
ETV5-AS1 | ENST00000453370.1 | n.173-548G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152060Hom.: 0 Cov.: 31
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000994 AC: 19AN: 191180Hom.: 0 AF XY: 0.000123 AC XY: 13AN XY: 105566
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GnomAD4 exome AF: 0.0000730 AC: 102AN: 1398086Hom.: 0 Cov.: 36 AF XY: 0.0000736 AC XY: 51AN XY: 693014
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GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152178Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 5AN XY: 74420
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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 | Apr 07, 2023 | The c.455C>A (p.P152Q) alteration is located in exon 7 (coding exon 6) of the ETV5 gene. This alteration results from a C to A substitution at nucleotide position 455, causing the proline (P) at amino acid position 152 to be replaced by a glutamine (Q). 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
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Uncertain
D;D
Polyphen
P;P
Vest4
MutPred
Loss of glycosylation at P152 (P = 0.0056);Loss of glycosylation at P152 (P = 0.0056);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Calibrated prediction
Score
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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