chr14-20891294-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_110261.4(LOC100507513):n.723-15551G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00694 in 216,494 control chromosomes in the GnomAD database, including 44 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 0.0070 ( 28 hom., cov: 31)
Exomes 𝑓: 0.0067 ( 16 hom. )
Consequence
LOC100507513
XR_110261.4 intron, non_coding_transcript
XR_110261.4 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.371
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0986 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC100507513 | XR_110261.4 | n.723-15551G>A | 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: 0.00706 AC: 1066AN: 151054Hom.: 28 Cov.: 31
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GnomAD4 exome AF: 0.00669 AC: 437AN: 65324Hom.: 16 AF XY: 0.00623 AC XY: 206AN XY: 33070
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GnomAD4 genome ? AF: 0.00705 AC: 1065AN: 151170Hom.: 28 Cov.: 31 AF XY: 0.00917 AC XY: 678AN XY: 73940
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3478
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