3-27721936-G-GCGGCGCCTGCAGCGGCGGCGGCGC
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_001278182.2(EOMES):c.358_359insGCGCCGCCGCCGCTGCAGGCGCCG(p.Ala119_Ala120insGlyAlaAlaAlaAlaAlaGlyAla) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A120A) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 0)
Exomes 𝑓: 8.2e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
EOMES
NM_001278182.2 conservative_inframe_insertion
NM_001278182.2 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.62
Publications
0 publications found
Genes affected
EOMES (HGNC:3372): (eomesodermin) This gene belongs to the TBR1 (T-box brain protein 1) sub-family of T-box genes that share the common DNA-binding T-box domain. The encoded protein is a transcription factor which is crucial for embryonic development of mesoderm and the central nervous system in vertebrates. The protein may also be necessary for the differentiation of effector CD8+ T cells which are involved in defense against viral infections. A similar gene disrupted in mice is shown to be essential during trophoblast development and gastrulation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]
EOMES Gene-Disease associations (from GenCC):
- microcephaly-polymicrogyria-corpus callosum agenesis syndromeInheritance: AR Classification: SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001278182.2
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| EOMES | NM_001278182.2 | c.358_359insGCGCCGCCGCCGCTGCAGGCGCCG | p.Ala119_Ala120insGlyAlaAlaAlaAlaAlaGlyAla | conservative_inframe_insertion | Exon 1 of 6 | ENST00000449599.4 | NP_001265111.1 | |
| EOMES | NM_005442.4 | c.358_359insGCGCCGCCGCCGCTGCAGGCGCCG | p.Ala119_Ala120insGlyAlaAlaAlaAlaAlaGlyAla | conservative_inframe_insertion | Exon 1 of 6 | NP_005433.2 | ||
| EOMES | XM_005265510.5 | c.358_359insGCGCCGCCGCCGCTGCAGGCGCCG | p.Ala119_Ala120insGlyAlaAlaAlaAlaAlaGlyAla | conservative_inframe_insertion | Exon 1 of 7 | XP_005265567.1 | ||
| EOMES | NM_001278183.2 | c.-5+493_-5+494insGCGCCGCCGCCGCTGCAGGCGCCG | intron_variant | Intron 1 of 5 | NP_001265112.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| EOMES | ENST00000449599.4 | c.358_359insGCGCCGCCGCCGCTGCAGGCGCCG | p.Ala119_Ala120insGlyAlaAlaAlaAlaAlaGlyAla | conservative_inframe_insertion | Exon 1 of 6 | 1 | NM_001278182.2 | ENSP00000388620.1 | ||
| EOMES | ENST00000295743.8 | c.358_359insGCGCCGCCGCCGCTGCAGGCGCCG | p.Ala119_Ala120insGlyAlaAlaAlaAlaAlaGlyAla | conservative_inframe_insertion | Exon 1 of 6 | 1 | ENSP00000295743.4 | |||
| EOMES | ENST00000461503.2 | c.-5+493_-5+494insGCGCCGCCGCCGCTGCAGGCGCCG | intron_variant | Intron 1 of 5 | 2 | ENSP00000487112.1 |
Frequencies
GnomAD3 genomes 0.00000662 AC: 1AN: 151026Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
151026
Hom.:
Cov.:
0
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:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 8.24e-7 AC: 1AN: 1213120Hom.: 0 Cov.: 35 AF XY: 0.00000169 AC XY: 1AN XY: 591020 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
1213120
Hom.:
Cov.:
35
AF XY:
AC XY:
1
AN XY:
591020
show subpopulations
African (AFR)
AF:
AC:
0
AN:
23740
American (AMR)
AF:
AC:
0
AN:
9520
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
17262
East Asian (EAS)
AF:
AC:
0
AN:
26208
South Asian (SAS)
AF:
AC:
0
AN:
43446
European-Finnish (FIN)
AF:
AC:
0
AN:
41800
Middle Eastern (MID)
AF:
AC:
0
AN:
3352
European-Non Finnish (NFE)
AF:
AC:
1
AN:
998342
Other (OTH)
AF:
AC:
0
AN:
49450
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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6
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<30
30-35
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Age
GnomAD4 genome 0.00000662 AC: 1AN: 151026Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 73682 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
151026
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
73682
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41210
American (AMR)
AF:
AC:
0
AN:
15158
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3460
East Asian (EAS)
AF:
AC:
0
AN:
4990
South Asian (SAS)
AF:
AC:
0
AN:
4804
European-Finnish (FIN)
AF:
AC:
0
AN:
10432
Middle Eastern (MID)
AF:
AC:
0
AN:
306
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67684
Other (OTH)
AF:
AC:
0
AN:
2076
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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