6-31125550-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014068.3(PSORS1C1):c.-228-126A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,876 control chromosomes in the GnomAD database, including 19,054 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 0.49 ( 19054 hom., cov: 32)
Exomes 𝑓: 0.41 ( 11 hom. )
Failed GnomAD Quality Control
Consequence
PSORS1C1
NM_014068.3 intron
NM_014068.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.103
Publications
16 publications found
Genes affected
PSORS1C1 (HGNC:17202): (psoriasis susceptibility 1 candidate 1) This gene is one of several genes thought to confer susceptibility to psoriasis and systemic sclerosis, located on chromosome 6 near the major histocompatibility complex (MHC) class I region. [provided by RefSeq, Sep 2011]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.493 AC: 74766AN: 151758Hom.: 19036 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
74766
AN:
151758
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:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.407 AC: 48AN: 118Hom.: 11 AF XY: 0.372 AC XY: 32AN XY: 86 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
48
AN:
118
Hom.:
AF XY:
AC XY:
32
AN XY:
86
show subpopulations
African (AFR)
AF:
AC:
2
AN:
2
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
5
AN:
10
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
39
AN:
102
Other (OTH)
AF:
AC:
2
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.515
Heterozygous variant carriers
0
1
3
4
6
7
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.493 AC: 74831AN: 151876Hom.: 19054 Cov.: 32 AF XY: 0.493 AC XY: 36629AN XY: 74228 show subpopulations
GnomAD4 genome
AF:
AC:
74831
AN:
151876
Hom.:
Cov.:
32
AF XY:
AC XY:
36629
AN XY:
74228
show subpopulations
African (AFR)
AF:
AC:
25536
AN:
41410
American (AMR)
AF:
AC:
7951
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
AC:
2164
AN:
3468
East Asian (EAS)
AF:
AC:
3196
AN:
5150
South Asian (SAS)
AF:
AC:
2037
AN:
4822
European-Finnish (FIN)
AF:
AC:
4287
AN:
10540
Middle Eastern (MID)
AF:
AC:
165
AN:
294
European-Non Finnish (NFE)
AF:
AC:
28102
AN:
67916
Other (OTH)
AF:
AC:
1087
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1910
3820
5730
7640
9550
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1687
AN:
3478
ClinVar
Not reported inComputational 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
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