rs2234975
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1
The NM_012238.5(SIRT1):c.*1728C>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0584 in 152,590 control chromosomes in the GnomAD database, including 342 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 0.058 ( 341 hom., cov: 33)
Exomes 𝑓: 0.074 ( 1 hom. )
Consequence
SIRT1
NM_012238.5 3_prime_UTR
NM_012238.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.85
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 -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.15).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0839 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIRT1 | NM_012238.5 | c.*1728C>T | 3_prime_UTR_variant | 9/9 | ENST00000212015.11 | ||
SIRT1 | NM_001142498.2 | c.*1728C>T | 3_prime_UTR_variant | 8/8 | |||
SIRT1 | NM_001314049.2 | c.*1728C>T | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIRT1 | ENST00000212015.11 | c.*1728C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_012238.5 | P1 | ||
SIRT1 | ENST00000403579.1 | c.*1728C>T | 3_prime_UTR_variant | 6/6 | 1 | ||||
SIRT1 | ENST00000406900.5 | c.*1728C>T | 3_prime_UTR_variant | 7/7 | 2 | ||||
SIRT1 | ENST00000432464.5 | c.*1728C>T | 3_prime_UTR_variant | 8/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0584 AC: 8873AN: 152040Hom.: 340 Cov.: 33
GnomAD3 genomes
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33
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GnomAD4 exome AF: 0.0741 AC: 32AN: 432Hom.: 1 Cov.: 0 AF XY: 0.0923 AC XY: 24AN XY: 260
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GnomAD4 genome ? AF: 0.0583 AC: 8872AN: 152158Hom.: 341 Cov.: 33 AF XY: 0.0556 AC XY: 4139AN XY: 74380
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at