XR_001737665.2:n.28-2807G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_001737665.2(LOC102724572):n.28-2807G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,898 control chromosomes in the GnomAD database, including 9,134 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 0.34 ( 9134 hom., cov: 32)
Consequence
LOC102724572
XR_001737665.2 intron
XR_001737665.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.04
Publications
4 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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes AF: 0.339 AC: 51456AN: 151782Hom.: 9127 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
51456
AN:
151782
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: 0.339 AC: 51485AN: 151898Hom.: 9134 Cov.: 32 AF XY: 0.336 AC XY: 24917AN XY: 74216 show subpopulations
GnomAD4 genome
AF:
AC:
51485
AN:
151898
Hom.:
Cov.:
32
AF XY:
AC XY:
24917
AN XY:
74216
show subpopulations
African (AFR)
AF:
AC:
11007
AN:
41424
American (AMR)
AF:
AC:
4868
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
1573
AN:
3468
East Asian (EAS)
AF:
AC:
902
AN:
5158
South Asian (SAS)
AF:
AC:
1266
AN:
4814
European-Finnish (FIN)
AF:
AC:
4189
AN:
10514
Middle Eastern (MID)
AF:
AC:
117
AN:
290
European-Non Finnish (NFE)
AF:
AC:
26497
AN:
67954
Other (OTH)
AF:
AC:
743
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1702
3404
5107
6809
8511
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
506
1012
1518
2024
2530
<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:
670
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.