chr5-150309610-C-T

Position:

• chr5-150309610-C-T

Variant summary

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

The ENST00000515301.2(ARSI):​c.-118-10998G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,180 control chromosomes in the GnomAD database, including 2,469 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 0.16 (2469 hom., cov: 32)
• Consequence: ARSI ENST00000515301.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

ARSI (HGNC:32521): (arylsulfatase family member I) This gene encodes a protein that belongs to a large family of sulfatases that hydrolyze sulfate esters and sulfamates. Members of this family play a role in several cellular processes, including hormone synthesis, cell signaling in development and degradation of macromolecules. The protein encoded by this gene is thought to be secreted, and to function in extracellular space. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARSI	ENST00000509146.1	c.-118-10998G>A		intron_variant		4		ENSP00000420955
ARSI	ENST00000515301.2	c.-118-10998G>A		intron_variant		4		ENSP00000426879

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23890 AN: 152062 Hom.: 2468 Cov.: 32

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.157 AC: 23890 AN: 152180 Hom.: 2469 Cov.: 32 AF XY: 0.153 AC XY: 11374 AN XY: 74408

Gnomad4 AFR AF: 0.0404

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0817

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.165

Alfa AF: 0.211 Hom.: 4840

Bravo AF: 0.148

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.9
DANN	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13184396; hg19: chr5-149689173;