XR_947985.1:n.102-16025C>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_947985.1(LOC105369474):n.102-16025C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,038 control chromosomes in the GnomAD database, including 37,004 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 0.69 ( 37004 hom., cov: 31)
Consequence
LOC105369474
XR_947985.1 intron
XR_947985.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.505
Publications
1 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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC105369474 | XR_947985.1 | n.102-16025C>G | intron_variant | Intron 2 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes AF: 0.695 AC: 105546AN: 151920Hom.: 36980 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
105546
AN:
151920
Hom.:
Cov.:
31
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: 0.695 AC: 105609AN: 152038Hom.: 37004 Cov.: 31 AF XY: 0.693 AC XY: 51490AN XY: 74282 show subpopulations
GnomAD4 genome
AF:
AC:
105609
AN:
152038
Hom.:
Cov.:
31
AF XY:
AC XY:
51490
AN XY:
74282
show subpopulations
African (AFR)
AF:
AC:
33143
AN:
41490
American (AMR)
AF:
AC:
8770
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
2037
AN:
3466
East Asian (EAS)
AF:
AC:
3303
AN:
5154
South Asian (SAS)
AF:
AC:
3131
AN:
4824
European-Finnish (FIN)
AF:
AC:
7317
AN:
10564
Middle Eastern (MID)
AF:
AC:
206
AN:
294
European-Non Finnish (NFE)
AF:
AC:
45687
AN:
67962
Other (OTH)
AF:
AC:
1384
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1643
3287
4930
6574
8217
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2156
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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