rs2905403
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000468762.3(XACT):n.293+34716C>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 0.54 ( 12274 hom., 17860 hem., cov: 22)
Failed GnomAD Quality Control
Consequence
XACT
ENST00000468762.3 intron, non_coding_transcript
ENST00000468762.3 intron, non_coding_transcript
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0690
Genes affected
XACT (HGNC:45056): (X active specific transcript) This gene produces a spliced long non-coding RNA that is thought to play a role in the control of X-chromosome inactivation (XCI). This transcript has been shown to specifically coat the active X chromosome in human pluripotent cells. [provided by RefSeq, Mar 2015]
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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=-0.94).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XACT | ENST00000468762.3 | n.293+34716C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
XACT | ENST00000674361.1 | n.60384C>T | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.539 AC: 59360AN: 110086Hom.: 12279 Cov.: 22 AF XY: 0.551 AC XY: 17840AN XY: 32378
GnomAD3 genomes
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110086
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17840
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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: 0.539 AC: 59368AN: 110136Hom.: 12274 Cov.: 22 AF XY: 0.551 AC XY: 17860AN XY: 32438
GnomAD4 genome
?
Data not reliable, filtered out with message: InbreedingCoeff
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17860
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at