rs2236318
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012238.5(SIRT1):c.548-71T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 1,512,402 control chromosomes in the GnomAD database, including 195,200 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 0.38 ( 14003 hom., cov: 32)
Exomes 𝑓: 0.50 ( 181197 hom. )
Consequence
SIRT1
NM_012238.5 intron
NM_012238.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.31
Genes affected
SIRT1 (HGNC:14929): (sirtuin 1) This gene encodes a member of the sirtuin family of proteins, homologs to the yeast Sir2 protein. Members of the sirtuin family are characterized by a sirtuin core domain and grouped into four classes. The functions of human sirtuins have not yet been determined; however, yeast sirtuin proteins are known to regulate epigenetic gene silencing and suppress recombination of rDNA. Studies suggest that the human sirtuins may function as intracellular regulatory proteins with mono-ADP-ribosyltransferase activity. The protein encoded by this gene is included in class I of the sirtuin family. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2008]
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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=-0.73).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIRT1 | NM_012238.5 | c.548-71T>A | intron_variant | ENST00000212015.11 | |||
SIRT1 | NM_001142498.2 | c.-97+1278T>A | intron_variant | ||||
SIRT1 | NM_001314049.2 | c.-487-71T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIRT1 | ENST00000212015.11 | c.548-71T>A | intron_variant | 1 | NM_012238.5 | P1 | |||
SIRT1 | ENST00000432464.5 | c.-97+1278T>A | intron_variant | 5 | |||||
SIRT1 | ENST00000473922.1 | n.333+1278T>A | intron_variant, non_coding_transcript_variant | 4 | |||||
SIRT1 | ENST00000497639.5 | n.337-71T>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.383 AC: 58159AN: 151970Hom.: 14007 Cov.: 32
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GnomAD4 exome AF: 0.502 AC: 682800AN: 1360314Hom.: 181197 AF XY: 0.498 AC XY: 333393AN XY: 669968
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GnomAD4 genome ? AF: 0.382 AC: 58144AN: 152088Hom.: 14003 Cov.: 32 AF XY: 0.377 AC XY: 27988AN XY: 74332
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at