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GeneBe

11-128486082-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_001143820.2(ETS1):c.600G>A(p.Ser200=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00252 in 1,607,380 control chromosomes in the GnomAD database, including 75 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0026 ( 73 hom. )

Consequence

ETS1
NM_001143820.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.888
Variant links:
Genes affected
ETS1 (HGNC:3488): (ETS proto-oncogene 1, transcription factor) This gene encodes a member of the ETS family of transcription factors, which are defined by the presence of a conserved ETS DNA-binding domain that recognizes the core consensus DNA sequence GGAA/T in target genes. These proteins function either as transcriptional activators or repressors of numerous genes, and are involved in stem cell development, cell senescence and death, and tumorigenesis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Jul 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.21).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-128486082-C-T is Benign according to our data. Variant chr11-128486082-C-T is described in ClinVar as [Benign]. Clinvar id is 777426.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.888 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00198 (301/152052) while in subpopulation SAS AF= 0.0357 (172/4816). AF 95% confidence interval is 0.0314. There are 2 homozygotes in gnomad4. There are 192 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 301 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ETS1NM_001143820.2 linkuse as main transcriptc.600G>A p.Ser200= synonymous_variant 6/10 ENST00000392668.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ETS1ENST00000392668.8 linkuse as main transcriptc.600G>A p.Ser200= synonymous_variant 6/101 NM_001143820.2 P14921-3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00198
AC:
301
AN:
151934
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000145
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00112
Gnomad ASJ
AF:
0.00980
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0357
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00101
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.00471
AC:
1183
AN:
251168
Hom.:
24
AF XY:
0.00633
AC XY:
859
AN XY:
135730
show subpopulations
Gnomad AFR exome
AF:
0.000123
Gnomad AMR exome
AF:
0.000550
Gnomad ASJ exome
AF:
0.00526
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0321
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000951
Gnomad OTH exome
AF:
0.00294
GnomAD4 exome
AF:
0.00258
AC:
3749
AN:
1455328
Hom.:
73
Cov.:
28
AF XY:
0.00356
AC XY:
2581
AN XY:
724542
show subpopulations
Gnomad4 AFR exome
AF:
0.000240
Gnomad4 AMR exome
AF:
0.000470
Gnomad4 ASJ exome
AF:
0.00556
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0321
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.000541
Gnomad4 OTH exome
AF:
0.00291
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00198
AC:
301
AN:
152052
Hom.:
2
Cov.:
32
AF XY:
0.00258
AC XY:
192
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.000145
Gnomad4 AMR
AF:
0.00111
Gnomad4 ASJ
AF:
0.00980
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0357
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00101
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00131
Hom.:
0
Bravo
AF:
0.000971
Asia WGS
AF:
0.00982
AC:
34
AN:
3478
EpiCase
AF:
0.00158
EpiControl
AF:
0.00101

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 submitterclinical testingInvitaeJul 31, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.21
Cadd
Benign
16
Dann
Benign
0.66

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs149636924; hg19: chr11-128355977; API