6-31129676-T-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.13+31T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 779,170 control chromosomes in the GnomAD database, including 217,178 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 0.76 ( 44837 hom., cov: 32)
Exomes 𝑓: 0.74 ( 172341 hom. )
Consequence
PSORS1C1
NM_014068.3 intron
NM_014068.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.48
Publications
20 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=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.764 AC: 116084AN: 151954Hom.: 44801 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
116084
AN:
151954
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: 0.741 AC: 180887AN: 244184 AF XY: 0.746 show subpopulations
GnomAD2 exomes
AF:
AC:
180887
AN:
244184
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: 0.737 AC: 462332AN: 627098Hom.: 172341 Cov.: 0 AF XY: 0.743 AC XY: 253892AN XY: 341700 show subpopulations
GnomAD4 exome
AF:
AC:
462332
AN:
627098
Hom.:
Cov.:
0
AF XY:
AC XY:
253892
AN XY:
341700
show subpopulations
African (AFR)
AF:
AC:
15140
AN:
17680
American (AMR)
AF:
AC:
28933
AN:
43670
Ashkenazi Jewish (ASJ)
AF:
AC:
17031
AN:
20958
East Asian (EAS)
AF:
AC:
31486
AN:
36034
South Asian (SAS)
AF:
AC:
57332
AN:
69730
European-Finnish (FIN)
AF:
AC:
32939
AN:
51996
Middle Eastern (MID)
AF:
AC:
3354
AN:
4148
European-Non Finnish (NFE)
AF:
AC:
251326
AN:
349816
Other (OTH)
AF:
AC:
24791
AN:
33066
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.483
Heterozygous variant carriers
0
5806
11613
17419
23226
29032
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
1366
2732
4098
5464
6830
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.764 AC: 116173AN: 152072Hom.: 44837 Cov.: 32 AF XY: 0.762 AC XY: 56618AN XY: 74336 show subpopulations
GnomAD4 genome
AF:
AC:
116173
AN:
152072
Hom.:
Cov.:
32
AF XY:
AC XY:
56618
AN XY:
74336
show subpopulations
African (AFR)
AF:
AC:
35643
AN:
41496
American (AMR)
AF:
AC:
11244
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
2836
AN:
3470
East Asian (EAS)
AF:
AC:
4611
AN:
5176
South Asian (SAS)
AF:
AC:
3984
AN:
4826
European-Finnish (FIN)
AF:
AC:
6631
AN:
10556
Middle Eastern (MID)
AF:
AC:
226
AN:
294
European-Non Finnish (NFE)
AF:
AC:
48786
AN:
67960
Other (OTH)
AF:
AC:
1608
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1363
2726
4089
5452
6815
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
862
1724
2586
3448
4310
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2825
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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