chr10-67891029-CAA-C

Variant names:

• chr10-67891029-CAA-C
• rs11327756
• NM_012238.5:c.790-360_790-359delAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_012238.5(SIRT1):​c.790-360_790-359delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.036 (325 hom., cov: 0)
• Consequence: SIRT1 NM_012238.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012238.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIRT1	NM_012238.5	MANE Select	c.790-360_790-359delAA		intron	N/A	NP_036370.2
	SIRT1	NM_001142498.2		c.-96-360_-96-359delAA		intron	N/A	NP_001135970.1
	SIRT1	NM_001314049.2		c.-245-360_-245-359delAA		intron	N/A	NP_001300978.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIRT1	ENST00000212015.11	TSL:1 MANE Select	c.790-372_790-371delAA		intron	N/A	ENSP00000212015.6
	SIRT1	ENST00000923649.1		c.790-372_790-371delAA		intron	N/A	ENSP00000593708.1
	SIRT1	ENST00000959939.1		c.790-372_790-371delAA		intron	N/A	ENSP00000629998.1

Frequencies

GnomAD3 genomes AF: 0.0364 AC: 3658 AN: 100376 Hom.: 323 Cov.: 0

Gnomad AFR AF: 0.00629

Gnomad AMI AF: 0.0364

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.00668

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.00885

Gnomad NFE AF: 0.00415

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0365 AC: 3661 AN: 100384 Hom.: 325 Cov.: 0 AF XY: 0.0438 AC XY: 2092 AN XY: 47750

African (AFR) AF: 0.00628 AC: 177 AN: 28184

American (AMR) AF: 0.0874 AC: 865 AN: 9894

Ashkenazi Jewish (ASJ) AF: 0.00668 AC: 16 AN: 2394

East Asian (EAS) AF: 0.407 AC: 1678 AN: 4120

South Asian (SAS) AF: 0.120 AC: 416 AN: 3454

European-Finnish (FIN) AF: 0.0548 AC: 254 AN: 4636

Middle Eastern (MID) AF: 0.00971 AC: 2 AN: 206

European-Non Finnish (NFE) AF: 0.00415 AC: 189 AN: 45514

Other (OTH) AF: 0.0304 AC: 41 AN: 1350

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11327756; hg19: chr10-69650787;