X-3006652-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001011719.2(ARSH):​c.40G>A​(p.Ala14Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000322 in 1,209,307 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 120 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00017 ( 0 hom., 6 hem., cov: 23)
Exomes 𝑓: 0.00034 ( 0 hom. 114 hem. )

Consequence

ARSH
NM_001011719.2 missense

Scores

2
11
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 8.05
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High Hemizygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARSHNM_001011719.2 linkc.40G>A p.Ala14Thr missense_variant Exon 1 of 9 ENST00000381130.3 NP_001011719.1 Q5FYA8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ARSHENST00000381130.3 linkc.40G>A p.Ala14Thr missense_variant Exon 1 of 9 1 NM_001011719.2 ENSP00000370522.3 Q5FYA8

Frequencies

GnomAD3 genomes
AF:
0.000171
AC:
19
AN:
111338
Hom.:
0
Cov.:
23
AF XY:
0.000179
AC XY:
6
AN XY:
33516
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000339
Gnomad OTH
AF:
0.000669
GnomAD3 exomes
AF:
0.000147
AC:
27
AN:
183166
Hom.:
0
AF XY:
0.000192
AC XY:
13
AN XY:
67606
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000330
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000338
AC:
371
AN:
1097917
Hom.:
0
Cov.:
29
AF XY:
0.000314
AC XY:
114
AN XY:
363279
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000247
Gnomad4 NFE exome
AF:
0.000406
Gnomad4 OTH exome
AF:
0.000608
GnomAD4 genome
AF:
0.000171
AC:
19
AN:
111390
Hom.:
0
Cov.:
23
AF XY:
0.000179
AC XY:
6
AN XY:
33578
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000339
Gnomad4 OTH
AF:
0.000661
Alfa
AF:
0.000243
Hom.:
8
Bravo
AF:
0.000140
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000149
AC:
1
ExAC
AF:
0.000173
AC:
21
EpiCase
AF:
0.000436
EpiControl
AF:
0.000297

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jun 21, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.40G>A (p.A14T) alteration is located in exon 1 (coding exon 1) of the ARSH gene. This alteration results from a G to A substitution at nucleotide position 40, causing the alanine (A) at amino acid position 14 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.19
BayesDel_addAF
Benign
-0.010
T
BayesDel_noAF
Uncertain
0.050
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.57
D
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Pathogenic
0.98
D
M_CAP
Uncertain
0.17
D
MetaRNN
Uncertain
0.44
T
MetaSVM
Pathogenic
0.97
D
MutationAssessor
Benign
1.4
L
PrimateAI
Uncertain
0.50
T
PROVEAN
Uncertain
-3.6
D
REVEL
Uncertain
0.52
Sift
Uncertain
0.0080
D
Sift4G
Uncertain
0.015
D
Polyphen
1.0
D
Vest4
0.44
MVP
0.57
MPC
0.62
ClinPred
0.35
T
GERP RS
1.8
Varity_R
0.52
gMVP
0.41

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs199938421; hg19: chrX-2924693; COSMIC: COSV66962475; API