Variant chr5-150296734-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001012301.4(ARSI):c.*480C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 153,632 control chromosomes in the GnomAD database, including 887 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 0.10 ( 884 hom., cov: 33)

Exomes 𝑓: 0.050 ( 3 hom. )

Consequence

ARSI
NM_001012301.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.167

Variant links:

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]

ARSI links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARSI	NM_001012301.4 link	c.*480C>A		3_prime_UTR_variant	2/2	ENST00000328668.8	NP_001012301.1	Q5FYB1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARSI	ENST00000328668 link	c.*480C>A		3_prime_UTR_variant	2/2	1	NM_001012301.4	ENSP00000333395.7		Q5FYB1-1

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15359

AN:

152134

Hom.:

883

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.0722

Gnomad ASJ

AF:

0.0553

Gnomad EAS

AF:

0.0365

Gnomad SAS

AF:

0.0317

Gnomad FIN

AF:

0.0845

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0931

Gnomad OTH

AF:

0.113

GnomAD4 exome

AF:

0.0500

AC:

AN:

1380

Hom.:

Cov.:

AF XY:

0.0567

AC XY:

AN XY:

776

show subpopulations

Gnomad4 AFR exome

AF:

0.0909

Gnomad4 AMR exome

AF:

0.00893

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.143

Gnomad4 NFE exome

AF:

0.0545

Gnomad4 OTH exome

AF:

0.0370

GnomAD4 genome

AF:

0.101

AC:

15380

AN:

152252

Hom.:

884

Cov.:

AF XY:

0.0984

AC XY:

7322

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.0721

Gnomad4 ASJ

AF:

0.0553

Gnomad4 EAS

AF:

0.0364

Gnomad4 SAS

AF:

0.0321

Gnomad4 FIN

AF:

0.0845

Gnomad4 NFE

AF:

0.0931

Gnomad4 OTH

AF:

0.111

Alfa

AF:

0.0800

Hom.:

244

Bravo

AF:

0.103

Asia WGS

AF:

0.0410

AC:

142

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.59

DANN

Benign

0.39

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over