21-44961649-T-A

Position:

• chr21-44961649-T-A

Variant summary

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

The NM_058190.4(SLX9):​c.352+1481T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,230 control chromosomes in the GnomAD database, including 2,390 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 0.17 (2390 hom., cov: 33)
• Consequence: SLX9 NM_058190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLX9	NM_058190.4	c.352+1481T>A		intron_variant		ENST00000291634.11	NP_478070.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLX9	ENST00000291634.11	c.352+1481T>A		intron_variant		1	NM_058190.4	ENSP00000291634
SLX9	ENST00000397826.8	c.307+1481T>A		intron_variant		1		ENSP00000380926	P1
SLX9	ENST00000458015.1	c.307+1481T>A		intron_variant		5		ENSP00000404964
SLX9	ENST00000479127.5	n.248+1481T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26231 AN: 152112 Hom.: 2391 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.172 AC: 26249 AN: 152230 Hom.: 2390 Cov.: 33 AF XY: 0.174 AC XY: 12914 AN XY: 74426

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.172

Alfa AF: 0.178 Hom.: 315

Bravo AF: 0.171

Asia WGS AF: 0.153 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.55

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: rs9981033; hg19: chr21-46381564;