rs31198
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000505828.5(PITX1-AS1):n.99+3455T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,038 control chromosomes in the GnomAD database, including 5,159 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 0.25 ( 5159 hom., cov: 33)
Consequence
PITX1-AS1
ENST00000505828.5 intron
ENST00000505828.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.229
Publications
36 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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PITX1-AS1 | NR_161235.1 | n.267+3455T>C | intron_variant | Intron 1 of 5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PITX1-AS1 | ENST00000505828.5 | n.99+3455T>C | intron_variant | Intron 1 of 4 | 4 | |||||
PITX1-AS1 | ENST00000507641.5 | n.159+3455T>C | intron_variant | Intron 1 of 4 | 3 | |||||
PITX1-AS1 | ENST00000624272.3 | n.261+3455T>C | intron_variant | Intron 1 of 5 | 2 | |||||
PITX1-AS1 | ENST00000806983.1 | n.119+3455T>C | intron_variant | Intron 1 of 4 |
Frequencies
GnomAD3 genomes AF: 0.247 AC: 37551AN: 151920Hom.: 5157 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
37551
AN:
151920
Hom.:
Cov.:
33
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: 0.247 AC: 37554AN: 152038Hom.: 5159 Cov.: 33 AF XY: 0.251 AC XY: 18623AN XY: 74318 show subpopulations
GnomAD4 genome
AF:
AC:
37554
AN:
152038
Hom.:
Cov.:
33
AF XY:
AC XY:
18623
AN XY:
74318
show subpopulations
African (AFR)
AF:
AC:
6962
AN:
41492
American (AMR)
AF:
AC:
4369
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
808
AN:
3472
East Asian (EAS)
AF:
AC:
2431
AN:
5158
South Asian (SAS)
AF:
AC:
1996
AN:
4802
European-Finnish (FIN)
AF:
AC:
2654
AN:
10570
Middle Eastern (MID)
AF:
AC:
62
AN:
294
European-Non Finnish (NFE)
AF:
AC:
17449
AN:
67950
Other (OTH)
AF:
AC:
497
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1420
2840
4259
5679
7099
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1595
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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