GeneBe

rs5899787

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The XR_001746881.2(LOC105376214):​n.721-77978dupA variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.69 ( 36700 hom., cov: 0)

Consequence

LOC105376214
XR_001746881.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.67

Publications

3 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt

There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt

There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes
AF:
0.690
AC:
104840
AN:
151932
Hom.:
36642
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.761
Gnomad AMI
AF:
0.644
Gnomad AMR
AF:
0.670
Gnomad ASJ
AF:
0.636
Gnomad EAS
AF:
0.957
Gnomad SAS
AF:
0.856
Gnomad FIN
AF:
0.659
Gnomad MID
AF:
0.658
Gnomad NFE
AF:
0.628
Gnomad OTH
AF:
0.682
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.690
AC:
104958
AN:
152050
Hom.:
36700
Cov.:
0
AF XY:
0.698
AC XY:
51897
AN XY:
74322
show subpopulations
African (AFR)
AF:
0.762
AC:
31591
AN:
41474
American (AMR)
AF:
0.670
AC:
10232
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.636
AC:
2205
AN:
3466
East Asian (EAS)
AF:
0.957
AC:
4953
AN:
5178
South Asian (SAS)
AF:
0.856
AC:
4128
AN:
4822
European-Finnish (FIN)
AF:
0.659
AC:
6954
AN:
10558
Middle Eastern (MID)
AF:
0.667
AC:
196
AN:
294
European-Non Finnish (NFE)
AF:
0.628
AC:
42667
AN:
67966
Other (OTH)
AF:
0.684
AC:
1445
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1656
3311
4967
6622
8278
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
820
1640
2460
3280
4100
<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:
0.672
Hom.:
4220
Bravo
AF:
0.692
Asia WGS
AF:
0.899
AC:
3121
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.7

Splicing

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

Publications

Other links and lift over

dbSNP: rs5899787; hg19: chr9-110893551; API