NM_170601.5:c.1482A>G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_170601.5(SIAE):c.1482A>G(p.Leu494Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,613,982 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 1 hom. )
Consequence
SIAE
NM_170601.5 synonymous
NM_170601.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.12
Publications
0 publications found
Genes affected
SIAE (HGNC:18187): (sialic acid acetylesterase) This gene encodes an enzyme which removes 9-O-acetylation modifications from sialic acids. Mutations in this gene are associated with susceptibility to autoimmune disease 6. Multiple transcript variants encoding different isoforms, found either in the cytosol or in the lysosome, have been found for this gene.[provided by RefSeq, Feb 2011]
SIAE Gene-Disease associations (from GenCC):
- autoimmune disease, susceptibility to, 6Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 11-124637041-T-C is Benign according to our data. Variant chr11-124637041-T-C is described in ClinVar as [Benign]. Clinvar id is 1618064.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-3.12 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SIAE | NM_170601.5 | c.1482A>G | p.Leu494Leu | synonymous_variant | Exon 10 of 10 | ENST00000263593.8 | NP_733746.1 | |
SIAE | NM_001199922.2 | c.1377A>G | p.Leu459Leu | synonymous_variant | Exon 12 of 12 | NP_001186851.1 | ||
SIAE | XM_047427132.1 | c.909A>G | p.Leu303Leu | synonymous_variant | Exon 7 of 7 | XP_047283088.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SIAE | ENST00000263593.8 | c.1482A>G | p.Leu494Leu | synonymous_variant | Exon 10 of 10 | 1 | NM_170601.5 | ENSP00000263593.3 | ||
SIAE | ENST00000618733.4 | c.1377A>G | p.Leu459Leu | synonymous_variant | Exon 12 of 12 | 1 | ENSP00000478211.1 | |||
SIAE | ENST00000545756.5 | c.1377A>G | p.Leu459Leu | synonymous_variant | Exon 11 of 11 | 5 | ENSP00000437877.1 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152092Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
29
AN:
152092
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.000306 AC: 77AN: 251444 AF XY: 0.000294 show subpopulations
GnomAD2 exomes
AF:
AC:
77
AN:
251444
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000133 AC: 195AN: 1461890Hom.: 1 Cov.: 31 AF XY: 0.000136 AC XY: 99AN XY: 727246 show subpopulations
GnomAD4 exome
AF:
AC:
195
AN:
1461890
Hom.:
Cov.:
31
AF XY:
AC XY:
99
AN XY:
727246
show subpopulations
African (AFR)
AF:
AC:
4
AN:
33480
American (AMR)
AF:
AC:
1
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
148
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
1
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53420
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
22
AN:
1112010
Other (OTH)
AF:
AC:
19
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.486
Heterozygous variant carriers
0
16
32
48
64
80
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.000191 AC: 29AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74300 show subpopulations
GnomAD4 genome
AF:
AC:
29
AN:
152092
Hom.:
Cov.:
32
AF XY:
AC XY:
17
AN XY:
74300
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41408
American (AMR)
AF:
AC:
1
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
AC:
18
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5196
South Asian (SAS)
AF:
AC:
0
AN:
4818
European-Finnish (FIN)
AF:
AC:
0
AN:
10608
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
9
AN:
68018
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.523
Heterozygous variant carriers
0
2
4
6
8
10
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 30, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.