21-38814278-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005239.6(ETS2):c.190G>A(p.Ala64Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0032 in 1,613,808 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0084 ( 12 hom., cov: 33)
Exomes 𝑓: 0.0027 ( 11 hom. )
Consequence
ETS2
NM_005239.6 missense
NM_005239.6 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -0.0690
Genes affected
ETS2 (HGNC:3489): (ETS proto-oncogene 2, transcription factor) This gene encodes a transcription factor which regulates genes involved in development and apoptosis. The encoded protein is also a protooncogene and shown to be involved in regulation of telomerase. A pseudogene of this gene is located on the X chromosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.003026694).
BP6
?
Variant 21-38814278-G-A is Benign according to our data. Variant chr21-38814278-G-A is described in ClinVar as [Benign]. Clinvar id is 786688.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0084 (1278/152180) while in subpopulation AFR AF= 0.0251 (1043/41508). AF 95% confidence interval is 0.0239. There are 12 homozygotes in gnomad4. There are 601 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1267 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ETS2 | NM_005239.6 | c.190G>A | p.Ala64Thr | missense_variant | 4/10 | ENST00000360938.8 | |
ETS2 | NM_001256295.2 | c.610G>A | p.Ala204Thr | missense_variant | 5/11 | ||
ETS2 | XM_005260935.2 | c.190G>A | p.Ala64Thr | missense_variant | 4/10 | ||
ETS2 | XM_017028290.2 | c.190G>A | p.Ala64Thr | missense_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ETS2 | ENST00000360938.8 | c.190G>A | p.Ala64Thr | missense_variant | 4/10 | 1 | NM_005239.6 | P1 | |
ETS2-AS1 | ENST00000663561.1 | n.535-853C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00833 AC: 1267AN: 152062Hom.: 11 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
1267
AN:
152062
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: 0.00305 AC: 767AN: 251236Hom.: 8 AF XY: 0.00255 AC XY: 346AN XY: 135784
GnomAD3 exomes
AF:
AC:
767
AN:
251236
Hom.:
AF XY:
AC XY:
346
AN XY:
135784
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: 0.00266 AC: 3882AN: 1461628Hom.: 11 Cov.: 31 AF XY: 0.00250 AC XY: 1817AN XY: 727130
GnomAD4 exome
AF:
AC:
3882
AN:
1461628
Hom.:
Cov.:
31
AF XY:
AC XY:
1817
AN XY:
727130
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: 0.00840 AC: 1278AN: 152180Hom.: 12 Cov.: 33 AF XY: 0.00808 AC XY: 601AN XY: 74400
GnomAD4 genome
?
AF:
AC:
1278
AN:
152180
Hom.:
Cov.:
33
AF XY:
AC XY:
601
AN XY:
74400
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.:
Bravo
AF:
TwinsUK
AF:
AC:
17
ALSPAC
AF:
AC:
7
ESP6500AA
AF:
AC:
107
ESP6500EA
AF:
AC:
20
ExAC
?
AF:
AC:
420
Asia WGS
AF:
AC:
4
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
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
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;.;T;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.;.
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
B;B;.;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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