rs11702328

Positions:

• chr21-44951044-C-T
• chr21-44951044-C-G

Variant summary

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

The NM_058190.4(SLX9):​c.283+7207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,896 control chromosomes in the GnomAD database, including 14,998 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 0.41 (14998 hom., cov: 31)
• Consequence: SLX9 NM_058190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLX9	NM_058190.4	c.283+7207C>T		intron_variant		ENST00000291634.11	NP_478070.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLX9	ENST00000291634.11	c.283+7207C>T		intron_variant		1	NM_058190.4	ENSP00000291634.6
SLX9	ENST00000397826.8	c.238+7252C>T		intron_variant		1		ENSP00000380926.3
SLX9	ENST00000458015.1	c.238+7252C>T		intron_variant		5		ENSP00000404964.1

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61563 AN: 151778 Hom.: 14997 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.405 AC: 61567 AN: 151896 Hom.: 14998 Cov.: 31 AF XY: 0.413 AC XY: 30653 AN XY: 74218

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.438

Alfa AF: 0.319 Hom.: 987

Bravo AF: 0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.68

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: rs11702328; hg19: chr21-46370959;