rs6593197
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_007060329.1(LOC105375284):n.892C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.018 in 152,318 control chromosomes in the GnomAD database, including 72 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 0.018 ( 72 hom., cov: 33)
Consequence
LOC105375284
XR_007060329.1 non_coding_transcript_exon
XR_007060329.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.21
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0594 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105375284 | XR_007060329.1 | n.892C>T | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.0179 AC: 2728AN: 152200Hom.: 72 Cov.: 33
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0180 AC: 2737AN: 152318Hom.: 72 Cov.: 33 AF XY: 0.0170 AC XY: 1269AN XY: 74474
GnomAD4 genome
?
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2737
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152318
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33
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1269
AN XY:
74474
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Asia WGS
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7
AN:
3478
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