rs860573
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_017521.3(FEV):c.357C>T(p.Gly119=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 1,613,502 control chromosomes in the GnomAD database, including 3,708 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 0.082 ( 1164 hom., cov: 33)
Exomes 𝑓: 0.029 ( 2544 hom. )
Consequence
FEV
NM_017521.3 synonymous
NM_017521.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.98
Genes affected
FEV (HGNC:18562): (FEV transcription factor, ETS family member) This gene belongs to the ETS transcription factor family. ETS family members have a highly conserved 85-amino acid ETS domain that binds purine-rich DNA sequences. The alanine-rich C-terminus of this gene indicates that it may act as a transcription repressor. This gene is exclusively expressed in neurons of the central serotonin (5-HT) system, a system implicated in the pathogeny of such psychiatric diseases as depression, anxiety, and eating disorders. In some types of Ewing tumors, this gene is fused to the Ewing sarcoma (EWS) gene following chromosome translocations. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP7
?
Synonymous conserved (PhyloP=1.98 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FEV | NM_017521.3 | c.357C>T | p.Gly119= | synonymous_variant | 3/3 | ENST00000295727.2 | |
FEV | XM_047444822.1 | c.72C>T | p.Gly24= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FEV | ENST00000295727.2 | c.357C>T | p.Gly119= | synonymous_variant | 3/3 | 1 | NM_017521.3 | P1 | |
LINC00608 | ENST00000627043.2 | n.1201+2647G>A | intron_variant, non_coding_transcript_variant | 5 | |||||
FEV | ENST00000470119.1 | n.475C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0815 AC: 12394AN: 152140Hom.: 1158 Cov.: 33
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GnomAD3 exomes AF: 0.0555 AC: 13847AN: 249650Hom.: 1056 AF XY: 0.0561 AC XY: 7589AN XY: 135366
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GnomAD4 exome AF: 0.0287 AC: 41938AN: 1461246Hom.: 2544 Cov.: 31 AF XY: 0.0313 AC XY: 22760AN XY: 726954
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GnomAD4 genome ? AF: 0.0816 AC: 12431AN: 152256Hom.: 1164 Cov.: 33 AF XY: 0.0838 AC XY: 6243AN XY: 74456
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at