rs62507090

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.335
Variant links:
Genes affected
SIRLNT (HGNC:53902): (SIRT1 regulating lncRNA tumor promoter)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
SIRLNTENST00000669842.1 linkuse as main transcriptn.71+18611A>G intron_variant, non_coding_transcript_variant
SIRLNTENST00000522486.1 linkuse as main transcriptn.125+18611A>G intron_variant, non_coding_transcript_variant 2

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs62507090; hg19: chr8-40182186; API