rs62507090

Positions:

• chr8-40324667-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000669842.1(SIRLNT):​n.71+18611A>G 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 0.0164 in 152,352 control chromosomes in the GnomAD database, including 34 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 0.016 (34 hom., cov: 33)
• Consequence: SIRLNT ENST00000669842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

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=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0164 (2506/152352) while in subpopulation NFE AF= 0.0254 (1725/68022). AF 95% confidence interval is 0.0244. There are 34 homozygotes in gnomad4. There are 1164 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 34 gene

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.71+18611A>G		intron_variant, non_coding_transcript_variant
SIRLNT	ENST00000522486.1	n.125+18611A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0164 AC: 2503 AN: 152234 Hom.: 34 Cov.: 33

Gnomad AFR AF: 0.00434

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.0116

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0254

Gnomad OTH AF: 0.0139

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

GnomAD4 genome AF: 0.0164 AC: 2506 AN: 152352 Hom.: 34 Cov.: 33 AF XY: 0.0156 AC XY: 1164 AN XY: 74514

Gnomad4 AFR AF: 0.00433

Gnomad4 AMR AF: 0.0106

Gnomad4 ASJ AF: 0.0282

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0197

Gnomad4 FIN AF: 0.0116

Gnomad4 NFE AF: 0.0254

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.0192 Hom.: 6

Bravo AF: 0.0164

Asia WGS AF: 0.00635 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.45
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62507090; hg19: chr8-40182186;