rs881317

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_058190.4(SLX9):​c.284-1521G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,190 control chromosomes in the GnomAD database, including 14,640 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 0.40 ( 14640 hom., cov: 34)

Consequence

SLX9
NM_058190.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.970
Variant links:
Genes affected
SLX9 (HGNC:15811): (SLX9 ribosome biogenesis factor) Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in nucleolus. Predicted to be part of 90S preribosome and preribosome, small subunit precursor. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLX9NM_058190.4 linkuse as main transcriptc.284-1521G>A intron_variant ENST00000291634.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLX9ENST00000291634.11 linkuse as main transcriptc.284-1521G>A intron_variant 1 NM_058190.4 Q9NSI2-1
SLX9ENST00000397826.8 linkuse as main transcriptc.239-1521G>A intron_variant 1 P1Q9NSI2-2
SLX9ENST00000458015.1 linkuse as main transcriptc.239-1521G>A intron_variant 5
SLX9ENST00000479127.5 linkuse as main transcriptn.179+155G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.400
AC:
60785
AN:
152072
Hom.:
14638
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.475
Gnomad AMR
AF:
0.449
Gnomad ASJ
AF:
0.448
Gnomad EAS
AF:
0.622
Gnomad SAS
AF:
0.647
Gnomad FIN
AF:
0.541
Gnomad MID
AF:
0.437
Gnomad NFE
AF:
0.496
Gnomad OTH
AF:
0.428
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.399
AC:
60789
AN:
152190
Hom.:
14640
Cov.:
34
AF XY:
0.408
AC XY:
30379
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.123
Gnomad4 AMR
AF:
0.449
Gnomad4 ASJ
AF:
0.448
Gnomad4 EAS
AF:
0.622
Gnomad4 SAS
AF:
0.647
Gnomad4 FIN
AF:
0.541
Gnomad4 NFE
AF:
0.496
Gnomad4 OTH
AF:
0.431
Alfa
AF:
0.442
Hom.:
2067
Bravo
AF:
0.375
Asia WGS
AF:
0.587
AC:
2038
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
4.7
DANN
Benign
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs881317; hg19: chr21-46378494; API