NM_001011719.2:c.396G>A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2

The NM_001011719.2(ARSH):​c.396G>A​(p.Pro132Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00329 in 1,209,358 control chromosomes in the GnomAD database, including 4 homozygotes. There are 1,192 hemizygotes in GnomAD. 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 0.0017 ( 0 hom., 47 hem., cov: 22)
Exomes 𝑓: 0.0035 ( 4 hom. 1145 hem. )

Consequence

ARSH
NM_001011719.2 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.57
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 Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP7
Synonymous conserved (PhyloP=-2.57 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 47 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARSHNM_001011719.2 linkc.396G>A p.Pro132Pro synonymous_variant Exon 4 of 9 ENST00000381130.3 NP_001011719.1 Q5FYA8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ARSHENST00000381130.3 linkc.396G>A p.Pro132Pro synonymous_variant Exon 4 of 9 1 NM_001011719.2 ENSP00000370522.3 Q5FYA8

Frequencies

GnomAD3 genomes
AF:
0.00168
AC:
187
AN:
111274
Hom.:
0
Cov.:
22
AF XY:
0.00140
AC XY:
47
AN XY:
33488
show subpopulations
Gnomad AFR
AF:
0.000490
Gnomad AMI
AF:
0.00442
Gnomad AMR
AF:
0.000289
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000167
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00309
Gnomad OTH
AF:
0.000668
GnomAD3 exomes
AF:
0.00175
AC:
321
AN:
182930
Hom.:
0
AF XY:
0.00166
AC XY:
112
AN XY:
67412
show subpopulations
Gnomad AFR exome
AF:
0.000836
Gnomad AMR exome
AF:
0.000182
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000125
Gnomad NFE exome
AF:
0.00365
Gnomad OTH exome
AF:
0.00110
GnomAD4 exome
AF:
0.00346
AC:
3794
AN:
1098029
Hom.:
4
Cov.:
31
AF XY:
0.00315
AC XY:
1145
AN XY:
363387
show subpopulations
Gnomad4 AFR exome
AF:
0.000720
Gnomad4 AMR exome
AF:
0.000227
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000247
Gnomad4 NFE exome
AF:
0.00433
Gnomad4 OTH exome
AF:
0.00250
GnomAD4 genome
AF:
0.00168
AC:
187
AN:
111329
Hom.:
0
Cov.:
22
AF XY:
0.00140
AC XY:
47
AN XY:
33553
show subpopulations
Gnomad4 AFR
AF:
0.000489
Gnomad4 AMR
AF:
0.000289
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000167
Gnomad4 NFE
AF:
0.00309
Gnomad4 OTH
AF:
0.000660
Alfa
AF:
0.000765
Hom.:
7
Bravo
AF:
0.00168
EpiCase
AF:
0.00354
EpiControl
AF:
0.00303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.7
DANN
Benign
0.63

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.

Other links and lift over

dbSNP: rs61746890; hg19: chrX-2933066; API