rs2522129

Positions:

• chr12-120310110-G-T

Variant summary

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

The NM_012240.3(SIRT4):​c.498-2346G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,814 control chromosomes in the GnomAD database, including 4,358 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 0.21 (4358 hom., cov: 30)
• Consequence: SIRT4 NM_012240.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

Genes affected

SIRT4 (HGNC:14932): (sirtuin 4) 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 IV of the sirtuin family. [provided by RefSeq, Jul 2008]

SIRT4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIRT4	NM_012240.3	c.498-2346G>T		intron_variant		ENST00000202967.4	NP_036372.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIRT4	ENST00000202967.4	c.498-2346G>T		intron_variant		1	NM_012240.3	ENSP00000202967.4
SIRT4	ENST00000537892.1	n.180-2474G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32410 AN: 151696 Hom.: 4358 Cov.: 30

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.170

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.214 AC: 32433 AN: 151814 Hom.: 4358 Cov.: 30 AF XY: 0.209 AC XY: 15509 AN XY: 74194

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0828

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.166

Alfa AF: 0.168 Hom.: 1207

Bravo AF: 0.221

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.63

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: rs2522129; hg19: chr12-120747913;