rs2739771
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000424333.6(SNHG14):n.381C>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 0.0135 in 499,316 control chromosomes in the GnomAD database, including 125 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 0.025 ( 92 hom., cov: 33)
Exomes 𝑓: 0.0084 ( 33 hom. )
Consequence
SNHG14
ENST00000424333.6 non_coding_transcript_exon
ENST00000424333.6 non_coding_transcript_exon
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0668 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNHG14 | NR_146177.1 | n.13308C>T | non_coding_transcript_exon_variant | 93/148 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNHG14 | ENST00000424333.6 | n.381C>T | non_coding_transcript_exon_variant | 5/54 | 1 | |||||
SNHG14 | ENST00000424208.5 | n.1931C>T | non_coding_transcript_exon_variant | 21/34 | 5 | |||||
SNHG14 | ENST00000653489.1 | n.295C>T | non_coding_transcript_exon_variant | 4/59 | ||||||
SNHG14 | ENST00000656420.1 | n.850C>T | non_coding_transcript_exon_variant | 7/57 |
Frequencies
GnomAD3 genomes AF: 0.0248 AC: 3780AN: 152180Hom.: 88 Cov.: 33
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GnomAD4 exome AF: 0.00842 AC: 2921AN: 347018Hom.: 33 Cov.: 0 AF XY: 0.00754 AC XY: 1507AN XY: 199972
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GnomAD4 genome AF: 0.0250 AC: 3811AN: 152298Hom.: 92 Cov.: 33 AF XY: 0.0249 AC XY: 1851AN XY: 74462
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at