ENST00000430058.2:n.331-11449G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000430058.2(PTCSC2):n.331-11449G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,858 control chromosomes in the GnomAD database, including 11,289 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 0.38 ( 11289 hom., cov: 32)
Consequence
PTCSC2
ENST00000430058.2 intron
ENST00000430058.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0310
Publications
2 publications found
Genes affected
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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTCSC2 | NR_147055.1 | n.778-9853G>A | intron_variant | Intron 5 of 10 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.376 AC: 57093AN: 151740Hom.: 11269 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
57093
AN:
151740
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.376 AC: 57154AN: 151858Hom.: 11289 Cov.: 32 AF XY: 0.372 AC XY: 27623AN XY: 74208 show subpopulations
GnomAD4 genome
AF:
AC:
57154
AN:
151858
Hom.:
Cov.:
32
AF XY:
AC XY:
27623
AN XY:
74208
show subpopulations
African (AFR)
AF:
AC:
14588
AN:
41416
American (AMR)
AF:
AC:
5415
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
1003
AN:
3468
East Asian (EAS)
AF:
AC:
238
AN:
5178
South Asian (SAS)
AF:
AC:
1261
AN:
4810
European-Finnish (FIN)
AF:
AC:
4600
AN:
10520
Middle Eastern (MID)
AF:
AC:
68
AN:
294
European-Non Finnish (NFE)
AF:
AC:
28961
AN:
67894
Other (OTH)
AF:
AC:
735
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
1846
3693
5539
7386
9232
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
546
1092
1638
2184
2730
<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:
661
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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