rs282071
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4BP6_ModerateBA1
The XR_007059680.1(LOC124901363):n.568C>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 0.631 in 151,974 control chromosomes in the GnomAD database, including 30,564 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.63 ( 30564 hom., cov: 32)
Consequence
LOC124901363
XR_007059680.1 non_coding_transcript_exon
XR_007059680.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.38
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.18).
BP6
?
Variant 6-90587361-C-T is Benign according to our data. Variant chr6-90587361-C-T is described in ClinVar as [Benign]. Clinvar id is 1228113.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124901363 | XR_007059680.1 | n.568C>T | non_coding_transcript_exon_variant | 1/2 | |||
LOC124901363 | XR_007059679.1 | n.149C>T | non_coding_transcript_exon_variant | 1/3 | |||
LOC124901363 | XR_007059681.1 | n.171C>T | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.631 AC: 95788AN: 151856Hom.: 30550 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.631 AC: 95835AN: 151974Hom.: 30564 Cov.: 32 AF XY: 0.626 AC XY: 46489AN XY: 74270
GnomAD4 genome
?
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151974
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32
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46489
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74270
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational 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