X-33978185-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000668394.1(ENSG00000233928):n.392-98281G>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 0.79 ( 24572 hom., 25065 hem., cov: 22)
Failed GnomAD Quality Control
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.330
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=-0.99).
BS2
?
High Homozygotes in GnomAd at 24578 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105373153 | XR_950542.4 | n.372-98281G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000668394.1 | n.392-98281G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.792 AC: 86646AN: 109438Hom.: 24578 Cov.: 22 AF XY: 0.788 AC XY: 25025AN XY: 31742
GnomAD3 genomes
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86646
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109438
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22
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25025
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31742
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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: 0.792 AC: 86674AN: 109486Hom.: 24572 Cov.: 22 AF XY: 0.788 AC XY: 25065AN XY: 31800
GnomAD4 genome
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Data not reliable, filtered out with message: InbreedingCoeff
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22
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25065
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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