21-44951044-C-T

Variant names:

• chr21-44951044-C-T
• rs11702328
• NM_058190.4:c.283+7207C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_058190.4. 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
	SLX9	NM_058190.4	MANE Select	c.283+7207C>T		intron	N/A	NP_478070.1	Q9NSI2-1
	SLX9	NM_001316983.2		c.283+7207C>T		intron	N/A	NP_001303912.1
	SLX9	NM_001316984.2		c.238+7252C>T		intron	N/A	NP_001303913.1	Q9NSI2-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLX9	ENST00000291634.11	TSL:1 MANE Select	c.283+7207C>T		intron	N/A	ENSP00000291634.6	Q9NSI2-1
	SLX9	ENST00000397826.8	TSL:1	c.238+7252C>T		intron	N/A	ENSP00000380926.3	Q9NSI2-2
	SLX9	ENST00000874000.1		c.283+7207C>T		intron	N/A	ENSP00000544059.1

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

African (AFR) AF: 0.125 AC: 5160 AN: 41444

American (AMR) AF: 0.454 AC: 6928 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1595 AN: 3472

East Asian (EAS) AF: 0.623 AC: 3214 AN: 5162

South Asian (SAS) AF: 0.643 AC: 3092 AN: 4812

European-Finnish (FIN) AF: 0.541 AC: 5696 AN: 10536

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34398 AN: 67908

Other (OTH) AF: 0.438 AC: 922 AN: 2104

Alfa AF: 0.319 Hom.: 987

Bravo AF: 0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.68
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11702328; hg19: chr21-46370959;