rs434421
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005239.6(ETS2):c.1195-361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 152,328 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0015 ( 1 hom., cov: 33)
Consequence
ETS2
NM_005239.6 intron
NM_005239.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.246
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BS2
?
High AC in GnomAd4 at 225 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ETS2 | NM_005239.6 | c.1195-361C>T | intron_variant | ENST00000360938.8 | |||
ETS2 | NM_001256295.2 | c.1615-361C>T | intron_variant | ||||
ETS2 | XM_005260935.2 | c.1195-361C>T | intron_variant | ||||
ETS2 | XM_017028290.2 | c.1195-361C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ETS2 | ENST00000360938.8 | c.1195-361C>T | intron_variant | 1 | NM_005239.6 | P1 | |||
ETS2-AS1 | ENST00000663561.1 | n.535-8888G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00148 AC: 225AN: 152210Hom.: 1 Cov.: 33
GnomAD3 genomes
?
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225
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152210
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00148 AC: 225AN: 152328Hom.: 1 Cov.: 33 AF XY: 0.00142 AC XY: 106AN XY: 74492
GnomAD4 genome
?
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225
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152328
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33
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106
AN XY:
74492
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3
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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