rs968431
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001012301.4(ARSI):c.-274T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000566 in 176,802 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)
Exomes 𝑓: 0.0000057 ( 0 hom. )
Consequence
ARSI
NM_001012301.4 5_prime_UTR
NM_001012301.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.416
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARSI | NM_001012301.4 | c.-274T>G | 5_prime_UTR_variant | 1/2 | ENST00000328668.8 | NP_001012301.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARSI | ENST00000328668.8 | c.-274T>G | 5_prime_UTR_variant | 1/2 | 1 | NM_001012301.4 | ENSP00000333395.7 | |||
ARSI | ENST00000515301.2 | c.-118-4035T>G | intron_variant | 4 | ENSP00000426879.2 | |||||
ARSI | ENST00000509146.1 | c.-118-4035T>G | intron_variant | 4 | ENSP00000420955.1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
GnomAD4 exome AF: 0.00000566 AC: 1AN: 176802Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0AN XY: 89696
GnomAD4 exome
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176802
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2
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0
AN XY:
89696
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GnomAD4 genome Cov.: 34
GnomAD4 genome
Cov.:
34
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at