GeneBe

rs925488

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000430058.2(PTCSC2):​n.330+21731C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,056 control chromosomes in the GnomAD database, including 39,509 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 0.72 ( 39509 hom., cov: 31)

Consequence

PTCSC2
ENST00000430058.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.602

Publications

13 publications found
Variant links:
Genes affected
PTCSC2 (HGNC:44086): (papillary thyroid carcinoma susceptibility candidate 2)

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=-0.87).
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
PTCSC2NR_147055.1 linkn.777+20142C>T intron_variant Intron 5 of 10

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PTCSC2ENST00000430058.2 linkn.330+21731C>T intron_variant Intron 2 of 2 2
PTCSC2ENST00000648027.1 linkn.470+20142C>T intron_variant Intron 3 of 4
PTCSC2ENST00000648505.1 linkn.330+21731C>T intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.717
AC:
108893
AN:
151938
Hom.:
39484
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.802
Gnomad AMI
AF:
0.479
Gnomad AMR
AF:
0.708
Gnomad ASJ
AF:
0.678
Gnomad EAS
AF:
0.890
Gnomad SAS
AF:
0.773
Gnomad FIN
AF:
0.669
Gnomad MID
AF:
0.712
Gnomad NFE
AF:
0.662
Gnomad OTH
AF:
0.719
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.717
AC:
108970
AN:
152056
Hom.:
39509
Cov.:
31
AF XY:
0.720
AC XY:
53541
AN XY:
74328
show subpopulations
African (AFR)
AF:
0.802
AC:
33264
AN:
41478
American (AMR)
AF:
0.708
AC:
10817
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.678
AC:
2353
AN:
3470
East Asian (EAS)
AF:
0.890
AC:
4612
AN:
5180
South Asian (SAS)
AF:
0.772
AC:
3724
AN:
4824
European-Finnish (FIN)
AF:
0.669
AC:
7061
AN:
10548
Middle Eastern (MID)
AF:
0.711
AC:
209
AN:
294
European-Non Finnish (NFE)
AF:
0.662
AC:
44979
AN:
67960
Other (OTH)
AF:
0.717
AC:
1516
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1514
3029
4543
6058
7572
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
834
1668
2502
3336
4170
<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:
0.688
Hom.:
15433
Bravo
AF:
0.724
Asia WGS
AF:
0.801
AC:
2789
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.16
DANN
Benign
0.59
PhyloP100
-0.60

Splicing

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

Publications

Other links and lift over

dbSNP: rs925488; hg19: chr9-100546391; API