4-113942550-T-C

Variant names:

• chr4-113942550-T-C
• rs7658266
• NM_024590.4:c.398+35887A>G

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+35887A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 151,926 control chromosomes in the GnomAD database, including 50,226 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 0.81 (50226 hom., cov: 31)
• Consequence: ARSJ NM_024590.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARSJ	NM_024590.4	c.398+35887A>G		intron_variant	Intron 1 of 1	ENST00000315366.8	NP_078866.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARSJ	ENST00000315366.8	c.398+35887A>G		intron_variant	Intron 1 of 1	1	NM_024590.4	ENSP00000320219.7
ARSJ	ENST00000509829.1	n.399-35805A>G		intron_variant	Intron 2 of 3	1		ENSP00000421327.1
ARSJ	ENST00000636527.1	n.399+27925A>G		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123120 AN: 151810 Hom.: 50174 Cov.: 31

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.811 AC: 123227 AN: 151926 Hom.: 50226 Cov.: 31 AF XY: 0.813 AC XY: 60311 AN XY: 74226

African (AFR) AF: 0.894 AC: 37113 AN: 41498

American (AMR) AF: 0.785 AC: 11950 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2425 AN: 3462

East Asian (EAS) AF: 0.802 AC: 4104 AN: 5116

South Asian (SAS) AF: 0.834 AC: 4015 AN: 4816

European-Finnish (FIN) AF: 0.804 AC: 8505 AN: 10580

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52444 AN: 67926

Other (OTH) AF: 0.805 AC: 1695 AN: 2106

Alfa AF: 0.793 Hom.: 16726

Bravo AF: 0.810

Asia WGS AF: 0.844 AC: 2935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.9
DANN	Benign	0.54
PhyloP100		-0.14
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: rs7658266; hg19: chr4-114863706;