rs17617724

Variant names:

• chr8-40306946-C-G
• rs17617724
• ENST00000521363.1:n.71-2163G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521363.1(SIRLNT):​n.71-2163G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,154 control chromosomes in the GnomAD database, including 2,077 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 0.14 (2077 hom., cov: 32)
• Consequence: SIRLNT ENST00000521363.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 1 publications found

Genes affected

SIRLNT (HGNC:53902): (SIRT1 regulating lncRNA tumor promoter)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521363.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIRLNT	ENST00000521363.1	TSL:2	n.71-2163G>C		intron	N/A
	SIRLNT	ENST00000522486.1	TSL:2	n.126-7492G>C		intron	N/A
	SIRLNT	ENST00000669842.2		n.159-7492G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21984 AN: 152036 Hom.: 2077 Cov.: 32

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.144 AC: 21985 AN: 152154 Hom.: 2077 Cov.: 32 AF XY: 0.145 AC XY: 10800 AN XY: 74358

African (AFR) AF: 0.0494 AC: 2051 AN: 41534

American (AMR) AF: 0.0900 AC: 1376 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3470

East Asian (EAS) AF: 0.0601 AC: 311 AN: 5174

South Asian (SAS) AF: 0.0956 AC: 461 AN: 4820

European-Finnish (FIN) AF: 0.270 AC: 2852 AN: 10548

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14282 AN: 67996

Other (OTH) AF: 0.117 AC: 248 AN: 2114

Alfa AF: 0.181 Hom.: 396

Bravo AF: 0.124

Asia WGS AF: 0.0730 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs17617724; hg19: chr8-40164465;