5-150302647-A-G

Position:

• chr5-150302647-A-G

Variant summary

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

The NM_001012301.4(ARSI):​c.-274T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 328,504 control chromosomes in the GnomAD database, including 85,526 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 0.71 (38435 hom., cov: 34)
  • Exomes 𝑓: 0.73 (47091 hom.)
• Consequence: ARSI NM_001012301.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARSI	NM_001012301.4	c.-274T>C		5_prime_UTR_variant	1/2	ENST00000328668.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARSI	ENST00000328668.8	c.-274T>C		5_prime_UTR_variant	1/2	1	NM_001012301.4	P1
ARSI	ENST00000509146.1	c.-118-4035T>C		intron_variant		4
ARSI	ENST00000515301.2	c.-118-4035T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107955 AN: 152018 Hom.: 38414 Cov.: 34

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.695

GnomAD4 exome AF: 0.729 AC: 128539 AN: 176372 Hom.: 47091 Cov.: 2 AF XY: 0.729 AC XY: 65214 AN XY: 89494

Gnomad4 AFR exome AF: 0.675

Gnomad4 AMR exome AF: 0.619

Gnomad4 ASJ exome AF: 0.713

Gnomad4 EAS exome AF: 0.709

Gnomad4 SAS exome AF: 0.730

Gnomad4 FIN exome AF: 0.741

Gnomad4 NFE exome AF: 0.740

Gnomad4 OTH exome AF: 0.716

GnomAD4 genome AF: 0.710 AC: 108020 AN: 152132 Hom.: 38435 Cov.: 34 AF XY: 0.708 AC XY: 52629 AN XY: 74378

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.695

Alfa AF: 0.733 Hom.: 8481

Bravo AF: 0.698

Asia WGS AF: 0.712 AC: 2475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.7
DANN	Benign	0.78

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: rs968431; hg19: chr5-149682210;