Variant X-3010129-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001011719.2(ARSH):c.192C>T(p.Thr64Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,208,646 control chromosomes in the GnomAD database, including 5,004 homozygotes. There are 41,787 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.099 ( 432 hom., 3110 hem., cov: 22)

Exomes 𝑓: 0.11 ( 4572 hom. 38677 hem. )

Consequence

ARSH
NM_001011719.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -4.07

Variant links:

Genes affected

ARSH (HGNC:32488): (arylsulfatase family member H) Sulfatases, such as ARSH, hydrolyze sulfate esters from sulfated steroids, carbohydrates, proteoglycans, and glycolipids. They are involved in hormone biosynthesis, modulation of cell signaling, and degradation of macromolecules (Sardiello et al., 2005 [PubMed 16174644]).[supplied by OMIM, Mar 2008]

ARSH links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant X-3010129-C-T is Benign according to our data. Variant chrX-3010129-C-T is described in ClinVar as [Benign]. Clinvar id is 558977.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-4.07 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARSH	NM_001011719.2 linkuse as main transcript	c.192C>T	p.Thr64Thr	synonymous_variant	2/9	ENST00000381130.3	NP_001011719.1	Q5FYA8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARSH	ENST00000381130.3 linkuse as main transcript	c.192C>T	p.Thr64Thr	synonymous_variant	2/9	1	NM_001011719.2	ENSP00000370522.3		Q5FYA8

Frequencies

GnomAD3 genomes

AF:

0.0989

AC:

11020

AN:

111380

Hom.:

432

Cov.:

AF XY:

0.0924

AC XY:

3104

AN XY:

33596

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.0560

Gnomad AMR

AF:

0.0517

Gnomad ASJ

AF:

0.0736

Gnomad EAS

AF:

0.00922

Gnomad SAS

AF:

0.0639

Gnomad FIN

AF:

0.0866

Gnomad MID

AF:

0.134

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.0957

GnomAD3 exomes

AF:

0.0851

AC:

15484

AN:

182056

Hom.:

530

AF XY:

0.0859

AC XY:

5721

AN XY:

66620

show subpopulations

Gnomad AFR exome

AF:

0.108

Gnomad AMR exome

AF:

0.0314

Gnomad ASJ exome

AF:

0.0719

Gnomad EAS exome

AF:

0.00651

Gnomad SAS exome

AF:

0.0717

Gnomad FIN exome

AF:

0.0904

Gnomad NFE exome

AF:

0.116

Gnomad OTH exome

AF:

0.0808

GnomAD4 exome

AF:

0.107

AC:

117670

AN:

1097213

Hom.:

4572

Cov.:

AF XY:

0.107

AC XY:

38677

AN XY:

362701

show subpopulations

Gnomad4 AFR exome

AF:

0.106

Gnomad4 AMR exome

AF:

0.0355

Gnomad4 ASJ exome

AF:

0.0762

Gnomad4 EAS exome

AF:

0.00480

Gnomad4 SAS exome

AF:

0.0745

Gnomad4 FIN exome

AF:

0.0953

Gnomad4 NFE exome

AF:

0.118

Gnomad4 OTH exome

AF:

0.103

GnomAD4 genome

AF:

0.0989

AC:

11019

AN:

111433

Hom.:

432

Cov.:

AF XY:

0.0924

AC XY:

3110

AN XY:

33659

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.0516

Gnomad4 ASJ

AF:

0.0736

Gnomad4 EAS

AF:

0.00953

Gnomad4 SAS

AF:

0.0641

Gnomad4 FIN

AF:

0.0866

Gnomad4 NFE

AF:

0.118

Gnomad4 OTH

AF:

0.0939

Alfa

AF:

0.111

Hom.:

1191

Bravo

AF:

0.0969

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Apr 25, 2017	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.30

DANN

Benign

0.61

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