8-40299341-A-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0979 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521363.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIRLNT	ENST00000521363.1	TSL:2	n.281T>A		non_coding_transcript_exon	Exon 3 of 3
	SIRLNT	ENST00000522486.1	TSL:2	n.239T>A		non_coding_transcript_exon	Exon 2 of 2
	SIRLNT	ENST00000669842.2		n.272T>A		non_coding_transcript_exon	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0132 AC: 547 AN: 41538

American (AMR) AF: 0.0351 AC: 537 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.105 AC: 544 AN: 5170

South Asian (SAS) AF: 0.0901 AC: 435 AN: 4826

European-Finnish (FIN) AF: 0.0235 AC: 249 AN: 10610

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0351 AC: 2389 AN: 68008

Other (OTH) AF: 0.0384 AC: 81 AN: 2112

Alfa AF: 0.0126 Hom.: 9

Bravo AF: 0.0314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.73
PhyloP100		1.8
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2272773; hg19: chr8-40156860;