8-40299341-A-T

Variant names:

• chr8-40299341-A-T
• rs2272773
• ENST00000521363.1:n.281T>A

Variant summary

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

The ENST00000521363.1(SIRLNT):​n.281T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 152,220 control chromosomes in the GnomAD database, including 133 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 0.033 (133 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SIRLNT ENST00000521363.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0979 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.281T>A		non_coding_transcript_exon_variant	Exon 3 of 3	2
SIRLNT	ENST00000522486.1	n.239T>A		non_coding_transcript_exon_variant	Exon 2 of 2	2
SIRLNT	ENST00000669842.1	n.185T>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0328 AC: 4989 AN: 152102 Hom.: 133 Cov.: 33

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0905

Gnomad FIN AF: 0.0235

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0351

Gnomad OTH AF: 0.0392

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0328 AC: 4991 AN: 152220 Hom.: 133 Cov.: 33 AF XY: 0.0335 AC XY: 2493 AN XY: 74450

Gnomad4 AFR AF: 0.0132

Gnomad4 AMR AF: 0.0351

Gnomad4 ASJ AF: 0.0473

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.0901

Gnomad4 FIN AF: 0.0235

Gnomad4 NFE AF: 0.0351

Gnomad4 OTH AF: 0.0384

Alfa AF: 0.0126 Hom.: 9

Bravo AF: 0.0314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2272773; hg19: chr8-40156860;