rs17484427

Variant names:

• chr4-113948711-C-G
• rs17484427
• NM_024590.4:c.398+29726G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024590.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARSJ	NM_024590.4	MANE Select	c.398+29726G>C		intron	N/A	NP_078866.3
	ARSJ	NM_001354210.2		c.398+29726G>C		intron	N/A	NP_001341139.1
	ARSJ	NM_001354211.2		c.-1+21764G>C		intron	N/A	NP_001341140.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARSJ	ENST00000315366.8	TSL:1 MANE Select	c.398+29726G>C		intron	N/A	ENSP00000320219.7
	ARSJ	ENST00000509829.1	TSL:1	n.398+29726G>C		intron	N/A	ENSP00000421327.1
	ARSJ	ENST00000503013.2	TSL:5	n.1328-2296G>C		intron	N/A

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

African (AFR) AF: 0.0328 AC: 1360 AN: 41512

American (AMR) AF: 0.114 AC: 1734 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3466

East Asian (EAS) AF: 0.0946 AC: 487 AN: 5146

South Asian (SAS) AF: 0.0767 AC: 370 AN: 4822

European-Finnish (FIN) AF: 0.187 AC: 1968 AN: 10546

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9256 AN: 67954

Other (OTH) AF: 0.120 AC: 253 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.34
PhyloP100		-0.13
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: rs17484427; hg19: chr4-114869867;