rs17484427

chr4-113948711-C-G

Variant summary

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

The NM_024590.4(ARSJ):c.398+29726G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,010 control chromosomes in the GnomAD database, including 1,063 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 0.11 (1063 hom., cov: 32)
• Consequence: ARSJ NM_024590.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

Genes affected

ARSJ (HGNC:26286): (arylsulfatase family member J) Sulfatases (EC 3.1.5.6), such as ARSJ, hydrolyze sulfate esters from sulfated steroids, carbohydrates, proteoglycans, and glycolipids. They are involved in hormone biosynthesis, modulation of cell signaling, and degradation of macromolecules (Sardiello et al., 2005 [PubMed 16174644]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARSJ	NM_024590.4	c.398+29726G>C		intron_variant		ENST00000315366.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARSJ	ENST00000315366.8	c.398+29726G>C		intron_variant		1	NM_024590.4	P1
ARSJ	ENST00000509829.1	c.398+29726G>C		intron_variant, NMD_transcript_variant		1
ARSJ	ENST00000503013.2	n.1328-2296G>C		intron_variant, non_coding_transcript_variant		5
ARSJ	ENST00000636527.1	n.399+21764G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16254 AN: 151892 Hom.: 1065 Cov.: 32

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0948

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.107 AC: 16247 AN: 152010 Hom.: 1063 Cov.: 32 AF XY: 0.109 AC XY: 8066 AN XY: 74284

Gnomad4 AFR AF: 0.0328

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0946

Gnomad4 SAS AF: 0.0767

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.120

Alfa AF: 0.116 Hom.: 143

Bravo AF: 0.101

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
Dann	Benign	0.34

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: rs17484427; hg19: chr4-114869867;