GeneBe

rs60131261

Variant names:

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-22646_589-22643delTAAA 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 0.27 ( 5607 hom., cov: 20)

Consequence

POLR1HASP
ENST00000849678.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.237

Publications

9 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 = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
POLR1HASPENST00000849678.1 linkn.589-22646_589-22643delTAAA intron_variant Intron 3 of 4
POLR1HASPENST00000849679.1 linkn.65+7041_65+7044delTAAA intron_variant Intron 1 of 5
POLR1HASPENST00000849680.1 linkn.506-12812_506-12809delTAAA intron_variant Intron 4 of 4

Frequencies

GnomAD3 genomes
AF:
0.265
AC:
40200
AN:
151460
Hom.:
5607
Cov.:
20
show subpopulations
Gnomad AFR
AF:
0.208
Gnomad AMI
AF:
0.288
Gnomad AMR
AF:
0.256
Gnomad ASJ
AF:
0.189
Gnomad EAS
AF:
0.309
Gnomad SAS
AF:
0.166
Gnomad FIN
AF:
0.359
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.296
Gnomad OTH
AF:
0.242
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.265
AC:
40197
AN:
151574
Hom.:
5607
Cov.:
20
AF XY:
0.264
AC XY:
19579
AN XY:
74024
show subpopulations
African (AFR)
AF:
0.208
AC:
8599
AN:
41302
American (AMR)
AF:
0.256
AC:
3900
AN:
15226
Ashkenazi Jewish (ASJ)
AF:
0.189
AC:
656
AN:
3468
East Asian (EAS)
AF:
0.310
AC:
1595
AN:
5148
South Asian (SAS)
AF:
0.165
AC:
786
AN:
4766
European-Finnish (FIN)
AF:
0.359
AC:
3763
AN:
10472
Middle Eastern (MID)
AF:
0.207
AC:
60
AN:
290
European-Non Finnish (NFE)
AF:
0.296
AC:
20074
AN:
67890
Other (OTH)
AF:
0.239
AC:
503
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
1456
2912
4368
5824
7280
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
404
808
1212
1616
2020
<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:
0.290
Hom.:
816
Bravo
AF:
0.260
Asia WGS
AF:
0.203
AC:
701
AN:
3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.24

Splicing

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

Publications

Other links and lift over

dbSNP: rs60131261; hg19: chr6-29937335; API