rs4286653

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001012301.4(ARSI):​c.311+1367C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0975 in 152,280 control chromosomes in the GnomAD database, including 751 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 0.098 ( 751 hom., cov: 33)

Consequence

ARSI
NM_001012301.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.28
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ARSINM_001012301.4 linkuse as main transcriptc.311+1367C>T intron_variant ENST00000328668.8 NP_001012301.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ARSIENST00000328668.8 linkuse as main transcriptc.311+1367C>T intron_variant 1 NM_001012301.4 ENSP00000333395 P1Q5FYB1-1
ARSIENST00000509146.1 linkuse as main transcriptc.-118-2084C>T intron_variant 4 ENSP00000420955
ARSIENST00000515301.2 linkuse as main transcriptc.-118-2084C>T intron_variant 4 ENSP00000426879 Q5FYB1-2

Frequencies

GnomAD3 genomes
AF:
0.0975
AC:
14842
AN:
152162
Hom.:
750
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0859
Gnomad AMI
AF:
0.141
Gnomad AMR
AF:
0.0718
Gnomad ASJ
AF:
0.0559
Gnomad EAS
AF:
0.0685
Gnomad SAS
AF:
0.0606
Gnomad FIN
AF:
0.132
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.111
Gnomad OTH
AF:
0.106
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0975
AC:
14854
AN:
152280
Hom.:
751
Cov.:
33
AF XY:
0.0966
AC XY:
7193
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.0860
Gnomad4 AMR
AF:
0.0717
Gnomad4 ASJ
AF:
0.0559
Gnomad4 EAS
AF:
0.0688
Gnomad4 SAS
AF:
0.0609
Gnomad4 FIN
AF:
0.132
Gnomad4 NFE
AF:
0.111
Gnomad4 OTH
AF:
0.106
Alfa
AF:
0.107
Hom.:
1185
Bravo
AF:
0.0928
Asia WGS
AF:
0.0810
AC:
282
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.41
CADD
Benign
11
DANN
Benign
0.72

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: rs4286653; hg19: chr5-149680259; API