rs33955981

chr10-67901600-T-Cchr10-67901600-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012238.5(SIRT1):c.943-5190T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,052 control chromosomes in the GnomAD database, including 30,652 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 0.63 (30652 hom., cov: 32)
• Consequence: SIRT1 NM_012238.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIRT1	NM_012238.5	c.943-5190T>C		intron_variant		ENST00000212015.11
SIRT1	NM_001142498.2	c.58-5190T>C		intron_variant
SIRT1	NM_001314049.2	c.-92-4563T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIRT1	ENST00000212015.11	c.943-5190T>C		intron_variant		1	NM_012238.5	P1
SIRT1	ENST00000406900.5	c.-92-4563T>C		intron_variant		2
SIRT1	ENST00000432464.5	c.58-5190T>C		intron_variant		5
SIRT1	ENST00000473922.1	n.487-5190T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95142 AN: 151932 Hom.: 30631 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.623

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.626 AC: 95203 AN: 152052 Hom.: 30652 Cov.: 32 AF XY: 0.617 AC XY: 45863 AN XY: 74346

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.626

Alfa AF: 0.655 Hom.: 4666

Bravo AF: 0.622

Asia WGS AF: 0.389 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.0
Dann	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs33955981; hg19: chr10-69661358;