rs17617724

chr8-40306946-C-G

Variant summary

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

The ENST00000669842.1(SIRLNT):n.72-7492G>C variant causes a intron, non coding transcript 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 ENST00000669842.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIRLNT	ENST00000669842.1	n.72-7492G>C		intron_variant, non_coding_transcript_variant
SIRLNT	ENST00000521363.1	n.71-2163G>C		intron_variant, non_coding_transcript_variant		2
SIRLNT	ENST00000522486.1	n.126-7492G>C		intron_variant, non_coding_transcript_variant		2

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;