6-31129676-T-G

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

20 publications found
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PSORS1C1NM_014068.3 linkc.13+31T>G intron_variant Intron 3 of 5 ENST00000259881.10 NP_054787.2 Q9UIG5-1D2IYL0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PSORS1C1ENST00000259881.10 linkc.13+31T>G intron_variant Intron 3 of 5 1 NM_014068.3 ENSP00000259881.9 Q9UIG5-1

Frequencies

GnomAD3 genomes
AF:
0.764
AC:
116084
AN:
151954
Hom.:
44801
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.859
Gnomad AMI
AF:
0.664
Gnomad AMR
AF:
0.737
Gnomad ASJ
AF:
0.817
Gnomad EAS
AF:
0.891
Gnomad SAS
AF:
0.825
Gnomad FIN
AF:
0.628
Gnomad MID
AF:
0.766
Gnomad NFE
AF:
0.718
Gnomad OTH
AF:
0.764
GnomAD2 exomes
AF:
0.741
AC:
180887
AN:
244184
AF XY:
0.746
show subpopulations
Gnomad AFR exome
AF:
0.859
Gnomad AMR exome
AF:
0.650
Gnomad ASJ exome
AF:
0.815
Gnomad EAS exome
AF:
0.898
Gnomad FIN exome
AF:
0.629
Gnomad NFE exome
AF:
0.719
Gnomad OTH exome
AF:
0.753
GnomAD4 exome
AF:
0.737
AC:
462332
AN:
627098
Hom.:
172341
Cov.:
0
AF XY:
0.743
AC XY:
253892
AN XY:
341700
show subpopulations
African (AFR)
AF:
0.856
AC:
15140
AN:
17680
American (AMR)
AF:
0.663
AC:
28933
AN:
43670
Ashkenazi Jewish (ASJ)
AF:
0.813
AC:
17031
AN:
20958
East Asian (EAS)
AF:
0.874
AC:
31486
AN:
36034
South Asian (SAS)
AF:
0.822
AC:
57332
AN:
69730
European-Finnish (FIN)
AF:
0.633
AC:
32939
AN:
51996
Middle Eastern (MID)
AF:
0.809
AC:
3354
AN:
4148
European-Non Finnish (NFE)
AF:
0.718
AC:
251326
AN:
349816
Other (OTH)
AF:
0.750
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:
116173
AN:
152072
Hom.:
44837
Cov.:
32
AF XY:
0.762
AC XY:
56618
AN XY:
74336
show subpopulations
African (AFR)
AF:
0.859
AC:
35643
AN:
41496
American (AMR)
AF:
0.736
AC:
11244
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.817
AC:
2836
AN:
3470
East Asian (EAS)
AF:
0.891
AC:
4611
AN:
5176
South Asian (SAS)
AF:
0.826
AC:
3984
AN:
4826
European-Finnish (FIN)
AF:
0.628
AC:
6631
AN:
10556
Middle Eastern (MID)
AF:
0.769
AC:
226
AN:
294
European-Non Finnish (NFE)
AF:
0.718
AC:
48786
AN:
67960
Other (OTH)
AF:
0.762
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:
0.736
Hom.:
42498
Bravo
AF:
0.775
Asia WGS
AF:
0.812
AC:
2825
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.051
DANN
Benign
0.45
PhyloP100
-1.5
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs3130560; hg19: chr6-31097453; API