rs497387
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000419001.1(SALL4P5):n.1027A>G 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 0.558 in 169,924 control chromosomes in the GnomAD database, including 27,125 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 0.53 ( 22105 hom., cov: 35)
Exomes 𝑓: 0.76 ( 5020 hom. )
Consequence
SALL4P5
ENST00000419001.1 non_coding_transcript_exon
ENST00000419001.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.402
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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SALL4P5 | ENST00000419001.1 | n.1027A>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.534 AC: 81155AN: 152088Hom.: 22079 Cov.: 35
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GnomAD4 exome AF: 0.763 AC: 13519AN: 17716Hom.: 5020 Cov.: 0 AF XY: 0.760 AC XY: 6956AN XY: 9148
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GnomAD4 genome AF: 0.534 AC: 81225AN: 152208Hom.: 22105 Cov.: 35 AF XY: 0.530 AC XY: 39429AN XY: 74420
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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