rs6518206

chr21-44974217-A-G

Variant summary

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

The NM_058190.4(SLX9):c.569+952A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 151,990 control chromosomes in the GnomAD database, including 40,590 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 0.72 (40590 hom., cov: 33)
• Consequence: SLX9 NM_058190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLX9	NM_058190.4	c.569+952A>G		intron_variant		ENST00000291634.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLX9	ENST00000291634.11	c.569+952A>G		intron_variant		1	NM_058190.4
SLX9	ENST00000397826.8	c.524+952A>G		intron_variant		1		P1
SLX9	ENST00000479127.5	n.465+952A>G		intron_variant, non_coding_transcript_variant		3
SLX9	ENST00000485207.1	n.210+952A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109707 AN: 151874 Hom.: 40516 Cov.: 33

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.705

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.723 AC: 109840 AN: 151990 Hom.: 40590 Cov.: 33 AF XY: 0.724 AC XY: 53777 AN XY: 74266

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.709

Alfa AF: 0.666 Hom.: 12921

Bravo AF: 0.737

Asia WGS AF: 0.839 AC: 2920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.9
Dann	Benign	0.69

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

Other links and lift over

dbSNP: rs6518206; hg19: chr21-46394132;