rs2215100
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000674719.1(VENTXP1):n.622+114324C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.60 ( 14104 hom., 19160 hem., cov: 22)
Failed GnomAD Quality Control
Consequence
VENTXP1
ENST00000674719.1 intron, non_coding_transcript
ENST00000674719.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.712
Genes affected
VENTXP1 (HGNC:30900): (VENT homeobox pseudogene 1) Homeobox genes encode DNA-binding proteins, many of which are thought to be involved in early embryonic development. Homeobox genes encode a DNA-binding domain of 60 to 63 amino acids referred to as the homeodomain. This pseudogene is a member of the Vent homeobox gene family. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VENTXP1 | ENST00000674719.1 | n.622+114324C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.600 AC: 65521AN: 109203Hom.: 14109 Cov.: 22 AF XY: 0.606 AC XY: 19130AN XY: 31581
GnomAD3 genomes
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65521
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109203
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22
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19130
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31581
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.600 AC: 65548AN: 109251Hom.: 14104 Cov.: 22 AF XY: 0.606 AC XY: 19160AN XY: 31639
GnomAD4 genome
?
Data not reliable, filtered out with message: InbreedingCoeff
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19160
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31639
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at