rs62507090

Variant names:

• chr8-40324667-T-C
• rs62507090
• ENST00000522486.1:n.125+18611A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000522486.1(SIRLNT):​n.125+18611A>G variant causes a intron 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 ENST00000522486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• 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=-0.86).
• 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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 34 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522486.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIRLNT	ENST00000522486.1	TSL:2	n.125+18611A>G		intron	N/A
	SIRLNT	ENST00000669842.2		n.158+18611A>G		intron	N/A
	SIRLNT	ENST00000800127.1		n.167+18611A>G		intron	N/A

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

African (AFR) AF: 0.00433 AC: 180 AN: 41586

American (AMR) AF: 0.0106 AC: 163 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0282 AC: 98 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5194

South Asian (SAS) AF: 0.0197 AC: 95 AN: 4828

European-Finnish (FIN) AF: 0.0116 AC: 123 AN: 10626

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0254 AC: 1725 AN: 68022

Other (OTH) AF: 0.0137 AC: 29 AN: 2114

Alfa AF: 0.0225 Hom.: 69

Bravo AF: 0.0164

Asia WGS AF: 0.00635 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.45
DANN	Benign	0.56
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs62507090; hg19: chr8-40182186;