Variant chr5-150298288-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The ENST00000328668.8(ARSI):c.636T>C(p.Tyr212=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 1,613,410 control chromosomes in the GnomAD database, including 796,971 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 1.0 ( 75565 hom., cov: 33)

Exomes 𝑓: 0.99 ( 721406 hom. )

Consequence

ARSI
ENST00000328668.8 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.12

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 5-150298288-A-G is Benign according to our data. Variant chr5-150298288-A-G is described in ClinVar as [Benign]. Clinvar id is 1168278.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.12 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARSI	NM_001012301.4 linkuse as main transcript	c.636T>C	p.Tyr212=	synonymous_variant	2/2	ENST00000328668.8	NP_001012301.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARSI	ENST00000328668.8 linkuse as main transcript	c.636T>C	p.Tyr212=	synonymous_variant	2/2	1	NM_001012301.4	ENSP00000333395	P1	Q5FYB1-1
ARSI	ENST00000515301.2 linkuse as main transcript	c.207T>C	p.Tyr69=	synonymous_variant	2/2	4		ENSP00000426879		Q5FYB1-2
ARSI	ENST00000509146.1 linkuse as main transcript	c.207T>C	p.Tyr69=	synonymous_variant	2/2	4		ENSP00000420955

Frequencies

GnomAD3 genomes

AF:

0.996

AC:

151585

AN:

152166

Hom.:

75506

Cov.:

show subpopulations

Gnomad AFR

AF:

0.998

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.998

Gnomad ASJ

AF:

0.997

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.998

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.997

Gnomad NFE

AF:

0.993

Gnomad OTH

AF:

0.996

GnomAD3 exomes

AF:

0.996

AC:

246589

AN:

247480

Hom.:

122852

AF XY:

0.996

AC XY:

133789

AN XY:

134296

show subpopulations

Gnomad AFR exome

AF:

0.999

Gnomad AMR exome

AF:

0.998

Gnomad ASJ exome

AF:

0.996

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.999

Gnomad FIN exome

AF:

0.999

Gnomad NFE exome

AF:

0.994

Gnomad OTH exome

AF:

0.995

GnomAD4 exome

AF:

0.994

AC:

1451934

AN:

1461126

Hom.:

721406

Cov.:

AF XY:

0.994

AC XY:

722354

AN XY:

726834

show subpopulations

Gnomad4 AFR exome

AF:

0.999

Gnomad4 AMR exome

AF:

0.998

Gnomad4 ASJ exome

AF:

0.997

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.999

Gnomad4 FIN exome

AF:

0.999

Gnomad4 NFE exome

AF:

0.992

Gnomad4 OTH exome

AF:

0.995

GnomAD4 genome

AF:

0.996

AC:

151703

AN:

152284

Hom.:

75565

Cov.:

AF XY:

0.997

AC XY:

74211

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.998

Gnomad4 AMR

AF:

0.998

Gnomad4 ASJ

AF:

0.997

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.998

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.993

Gnomad4 OTH

AF:

0.996

Alfa

AF:

0.994

Hom.:

39595

Bravo

AF:

0.996

Asia WGS

AF:

0.999

AC:

3474

AN:

3478

EpiCase

AF:

0.993

EpiControl

AF:

0.994

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Spastic paraplegia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

0.027

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over