rs945048
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The XR_938423.3(NXTAR):n.81+6449A>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 0.87 ( 30664 hom., 27159 hem., cov: 21)
Failed GnomAD Quality Control
Consequence
NXTAR
XR_938423.3 intron, non_coding_transcript
XR_938423.3 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.481
Genes affected
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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=-0.96).
BS2
?
High Homozygotes in GnomAd at 30674 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NXTAR | XR_938423.3 | n.81+6449A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.868 AC: 94363AN: 108658Hom.: 30674 Cov.: 21 AF XY: 0.875 AC XY: 27130AN XY: 31014
GnomAD3 genomes
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108658
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.868 AC: 94376AN: 108709Hom.: 30664 Cov.: 21 AF XY: 0.874 AC XY: 27159AN XY: 31075
GnomAD4 genome
?
Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at