GeneBe

rs4016810

Variant names:

Variant summary

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

The XR_001747415.2(LOC107984219):​n.5354-10717_5354-10716delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.47 ( 17242 hom., cov: 0)

Consequence

LOC107984219
XR_001747415.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0580

Publications

0 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 = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC107984219XR_001747415.2 linkn.5354-10717_5354-10716delGT intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.470
AC:
71056
AN:
151290
Hom.:
17242
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.350
Gnomad AMI
AF:
0.540
Gnomad AMR
AF:
0.478
Gnomad ASJ
AF:
0.472
Gnomad EAS
AF:
0.605
Gnomad SAS
AF:
0.493
Gnomad FIN
AF:
0.595
Gnomad MID
AF:
0.462
Gnomad NFE
AF:
0.508
Gnomad OTH
AF:
0.470
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.469
AC:
71079
AN:
151408
Hom.:
17242
Cov.:
0
AF XY:
0.474
AC XY:
35046
AN XY:
73930
show subpopulations
African (AFR)
AF:
0.350
AC:
14445
AN:
41264
American (AMR)
AF:
0.477
AC:
7267
AN:
15224
Ashkenazi Jewish (ASJ)
AF:
0.472
AC:
1636
AN:
3464
East Asian (EAS)
AF:
0.605
AC:
3105
AN:
5130
South Asian (SAS)
AF:
0.495
AC:
2374
AN:
4798
European-Finnish (FIN)
AF:
0.595
AC:
6196
AN:
10416
Middle Eastern (MID)
AF:
0.466
AC:
137
AN:
294
European-Non Finnish (NFE)
AF:
0.508
AC:
34447
AN:
67812
Other (OTH)
AF:
0.468
AC:
984
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
1826
3652
5478
7304
9130
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
656
1312
1968
2624
3280
<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:
0.492
Hom.:
2269
Bravo
AF:
0.456
Asia WGS
AF:
0.516
AC:
1790
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.058

Splicing

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

Publications

Other links and lift over

dbSNP: rs4016810; hg19: chr10-32296233; API