rs17617724

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SIRLNT	ENST00000521363.1	n.71-2163G>C		intron_variant	Intron 1 of 2	2
SIRLNT	ENST00000522486.1	n.126-7492G>C		intron_variant	Intron 1 of 1	2
SIRLNT	ENST00000669842.1	n.72-7492G>C		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.0494

Gnomad4 AMR AF: 0.0900

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.0601

Gnomad4 SAS AF: 0.0956

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.117

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17617724; hg19: chr8-40164465;