chr5-150328215-A-G

Position:

• chr5-150328215-A-G

Variant summary

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

The ENST00000515301.2(ARSI):​c.-119+11063T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,304 control chromosomes in the GnomAD database, including 712 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 0.094 (712 hom., cov: 32)
• Consequence: ARSI ENST00000515301.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARSI	ENST00000509146.1	c.-119+10985T>C		intron_variant		4
ARSI	ENST00000515301.2	c.-119+11063T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14275 AN: 152186 Hom.: 714 Cov.: 32

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.0563

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.0900

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0899

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

GnomAD4 genome AF: 0.0937 AC: 14272 AN: 152304 Hom.: 712 Cov.: 32 AF XY: 0.0941 AC XY: 7005 AN XY: 74476

Gnomad4 AFR AF: 0.0989

Gnomad4 AMR AF: 0.0552

Gnomad4 ASJ AF: 0.0563

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.0805

Gnomad4 FIN AF: 0.0900

Gnomad4 NFE AF: 0.0930

Gnomad4 OTH AF: 0.0899

Alfa AF: 0.0903 Hom.: 747

Bravo AF: 0.0926

Asia WGS AF: 0.136 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.64
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11750343; hg19: chr5-149707778;